[Freesurfer] Possible to generate table of statistics for specific label?
Dear List Members, Is it possible to generate tables of volume / area / thickness information for a specific label that is not included in aparcstats or asegstats using command line code in freesurfer (e.g. the broadman areas)? If so, could someone point me to the instructions? Thank you for your time and consideration. Best wishes, Sal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Fwd: Freesurfer Digest, Vol 131, Issue 13
Dear Doug, Thank you for your email. I am running into trouble using mri_segstats - the command you sent (mri_segstats --i lh.thickness --slabel subject lh lh.BA3a.label --id 1 --sum table.dat) gave me the error: "No such file or directory mri_segstats: could not open label file lh.BA3a.label" I tried substituting a single subject in place of "subject" in the command you sent I get the same error. I confirmed that the lh.BA3a.label file is in the label subfolder for the individual subject. I would like to output the volume, thickness, and area for all the broadman areas (especially 35). Any advice you can provide on how to do this would be a great help. Thank you for all your help. Sal Date: Thu, 08 Jan 2015 11:37:11 -0500 From: Douglas N Greve Subject: Re: [Freesurfer] Possible to generate table of statistics for specific label? To: freesurfer@nmr.mgh.harvard.edu Message-ID: <54aeb237.9010...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed Yep, you can use somehting like mri_segstats --i lh.thickness --slabel subject lh lh.BA3a.label --id 1 --sum table.dat doug On 01/08/2015 08:50 AM, Salil Soman wrote: > Dear List Members, > > Is it possible to generate tables of volume / area / thickness > information for a specific label that is not included in aparcstats or > asegstats using command line code in freesurfer (e.g. the broadman > areas)? If so, could someone point me to the instructions? > > Thank you for your time and consideration. > > Best wishes, > > Sal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] using merge_stats_tables to merge broadman areas for multiple subjects.
Hi, Following earlier device from this list, I was able to run the merge_stats_tables command for a single subject as so: merge_stats_tables --inputs $SUBJECTS_DIR/SUBJ_ID1/stats/lh.BA.stats --all-segs --tablefile test_lh_BA_Stats_volumes.txt --meas volume But when I tried to pass a series of subjects: merge_stats_tables --inputs $SUBJECTS_DIR/SUBJ_ID1/stats/lh.BA.stats $SUBJECTS_DIR/SUBJ_ID2/stats/lh.BA.stats --all-segs --tablefile test_lh_BA_Stats_volumes.txt --meas volume I get the error "duplicate row found: BA1, not sure if identical data, therefore stopping!" Is there a way to use merge_stats_tables to combine the broadman area volumes for multiple subjects into 1 table? Thanks! -Sal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] freesurfer in patients with brain volume loss after old injury or infarcts
Hi, Is there an official thought on using freesurfer on cases were there is volume loss after old stroke, or surgery, or trauma? I have a number of cases were the results in general look reasonable for the remaining brain tissue, and was was wondering if it is valid to use that data for analyses? Best wishes, Salil ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] How best to review actual anatomic structures labelled under hippocampal subfield label?
Hi, I have a a few studies where I have performed the hippocamapl subfield analysis from FS 5.3, and have found some areas significant. One criticism I have heard is that the anatomic labels for FS hippocampal subfields are approximations based on landmarks and that they do not actually represent what they are named (e.g. hippocampal fissure). I am writing to ask if this is a generally accepted shortcoming of the method? Also, could someone point me to how to review the hippocamapl subfield label image and the actual anatomic (t1) region it overlies? Thank you for considering this question. Best wishes, Salil Soman, MD, MS ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] preferred method for generating appropriate bvecs for tracula
Hi Anastasia,
Thank you for this code piece. Is there a way to modify it so that set y's
sign gets flipped? (I have a dataset where its is acquired on GE (so the Y
row gets flipped)?
Thank you!
-Sal
On Wed, Aug 7, 2013 at 1:12 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:
>
> set x = `cat bvecs | awk '{if (NR==1) print}'`
> set y = `cat bvecs | awk '{if (NR==2) print}'`
> set z = `cat bvecs | awk '{if (NR==3) print}'`
>
> @ k = 1
> while ( $k <= `head -1 bvecs|wc -w` )
> echo $x[$k] $y[$k] $z[$k]
> @ k = $k + 1
> end
>
> I'd make sure though dcm2nii doesn't L-R flip the gradient vectors, I
> think there was a thread recently that suggested it might.
>
>
> On Wed, 7 Aug 2013, Salil Soman wrote:
>
> Hi,
>> I have dicoms that I turn to nifti using dcm2nii (with the default
>> settings plus anonymization option turned on [-a
>> y]). The bvec files it generates by default are 3 rows by n columns
>> (where n is b0 number + directions). I am under
>> the impression tracula requires this to be converted to a n row by 3
>> column file. 1) is this correct, 2) is there a
>> preferred way to perform this transformation on linux systems?
>>
>> Thanks you,
>>
>> -Sal
>>
>>
>>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>.
> If the e-mail was sent to you in error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
--
Salil Soman, MD, MS
Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory
Fellow - Palo Alto War Related Illness and Injury Study Center
WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System
___
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[Freesurfer] Etiv difference in difference in same patient
Hi, My understanding of etiv is that it is derived from the registration of a brain to atlas space and not actually derived from the freesurfer segmentation. I have a set of patients imaged at 2 time points that all have different etiv values between the first and second scan that are statistically significant. As there was no change in their skulls between scans, I am having difficulty understanding how this is possible. Can anyone suggest what I may be doing wrong? Best wishes, Salil ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Getting substantially different Etiv for same patients for consecutive scans
Hi, My understanding of etiv is that it is derived from the registration of a brain to atlas space and not actually derived from the freesurfer segmentation. I have a set of patients imaged at 2 time points that all have different etiv values between the first and second scan that are statistically significant. As there was no change in their skulls between scans, I am having difficulty understanding how this is possible. Can anyone suggest what I may be doing wrong? Best wishes, Salil ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Longitudinal freesurfer analysis question
Thank you Martin. Just to clarify, then it is not valid to compare values of single point analyses (e.g. hippocampal volume from freesurfer analysis of time point 1 subtracted from hippocampal volume of from freesurfer analysis of time point 2). Best wishes, -Salil On Mon, Nov 11, 2013 at 7:58 AM, Martin Reuter wrote: > Hi Salil, > > please send questions to the free surfer mailing list. > > If you used the longitudinal stream for processing the etiv should be the > same in all time points. It is computed in the 'base' = within subject > template once for the entire series. > It seems that you did not run your images through the longitudinal stream > if your etiv is different across time points. > > For longitudinal processing see here: > http://freesurfer.net/fswiki/LongitudinalProcessing > > Bes,t Martin > > On Nov 10, 2013, at 3:37 PM, Salil Soman wrote: > > Dear Dr. Reuter, > > I have performed freesurfer 5.3 with hippo subfields Analysis on patients > that have 2 consecutive scans (pre and post surgery). I have generated > Segstats statistics for each individual time point. I have noticed the > etiv is different on all of the cases for each time point (scan 1 is > different from 2). This has led me to worry that it may not be legitimate > to perform analyses of changes in volumes of structures by computing > differences in values between time points). I am writing to inquire if you > were familiar with /had an opinion regarding this matter. > > Best wishes, > > Salil Soman, MD, MS > Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory > Fellow - Palo Alto War Related Illness and Injury Study Center > WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care > System > > > - > Dr. Martin Reuter > Assistant in Neuroscience - Massachusetts General Hospital > Instructor in Neurology - Harvard Medical School > MGH / HMS / MIT > > A.A.Martinos Center for Biomedical Imaging > 149 Thirteenth Street, Suite 2301 > Charlestown, MA 02129 > > Phone: +1-617-724-5652 > Email: >mreu...@nmr.mgh.harvard.edu >reu...@mit.edu > Web : http://reuter.mit.edu > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Fwd: Minimum Dti directions and odf
Hi, I hope all is well. Was wondering if any of had heard of an explicit minimum number of DTI directions necessary for using odf / hardi modeling ? I have run a couple of data sets of 30 directions (+ 5 b0) through TRACULA, and have run this same data through diffusion toolkit using the hardi / odf model, with reasonable looking results. I was wondering if there was any specific reason why using these models with 30 directions would be considered in appropriate? Thanks! Sal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] How to get aparcstats2table to output thickness and other parameters
Hi, Is there a way to get aparcstats2table to output all of the information for each subject, including thickness values? Thank you, Salil ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] kvlQuantifyHippocampalSubfieldSegmentations Usage
Hi, Have been able to run kvlQuantifyHippocampalSubfieldSegmentations.sh to get hippocampal subfield segmentation number of voxels. How do I convert these values into volumes? I am guessing the voxel size of the original image is not the correct conversion factor. Also, I have not been able to find any details regarding the doPartialVolumedSegmentation vs doNonPartialVolumedSegmentation options for this code. Can anyone point me to more details of why one would use one method vs the other? Thanks, -Salil ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Units for Aparcstats2table for thickness and curvature
Hi, I am writing to confirm the units for aparcstats2table for thickness and thicknessSTD are mm, and curvature is radians. It would be a great help if this could be confirmed. Thank you. Salil ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] missing libnetcdf.so.6 on ubuntu for TRACULA
Dear Anastasia, I am using the latest tracula code (CentOS 6 64 bit on an ubuntu 13 machine) and FS 5.3 to rerun cases I had processed with the previous version of tracula using the new code and am getting the following errors: *freesurfer/bin/dmri_motion: error while loading shared libraries: libnetcdf.so.6: cannot open shared object file: No such file or directory* and also after the bvecs and bvals files are copied to the output directory: *xx: Subscript out of range.* I have set LD_LIBRARY_PATH to include /usr/lib (where libnetcdf.so.7.1.1 is located) and a separate directory where I have made a link from libnetcdf.so.6 to /usr/lib/libnetcdf.so.7.1.1. Any suggestions would be greatly appreciated. Best wishes, Sal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] possible to run freeview using other versions of libjpeg other than libjpeg.so.62?
Hi, My cluster environment is setup to use libjpeg turbo on ubuntu 13.04 (ends up with libjpeg.so.8.0.2 in the /usr/lib/x86_64-linux-gnu/ directory). Is there a way to get freeview to work with a different version of libjpeg (e.g. by making a symbolic link from libjpeg.so.62 to the libjpeg.so.8.0.2 file)? Thanks, -Sal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] possible to run freeview using other versions of libjpeg.so.62?
Hi, My cluster environment is setup to use libjpeg turbo on ubuntu 13.04 (ends up with libjpeg.so.8.0.2 in the /usr/lib/x86_64-linux-gnu/ directory). Is it possible to use this version of libjpeg to run freeview (it currently complaints that it cannot find libjpeg.so.62)? If so, can anyone provide info on what symbolic links or environment variables I need to create to do this? Thank you. Salil ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Change in Tracula ability to use bvec / bval file containing zeros for b0 images?
Hi, I have been trying to rerun cases through the new (12/13) tracula code, which I had successfully ran through the pre 12/13 code. While I am still trying to sort out the libnetcdf.so.6 issue on our cluster, I also noticed that cases which I ran using the bvec and bval files including 0's for the b0 files were processed with the old code, but result in a xx:subscript out of range error in the current code. Removing the b0 entries fixed the problem and the remainder of the processing (other than the part requiring libnetcdf.so.6) works. I did notice that the bvecs and bval files in the diffusion tutorial do include the b0 0. Does the current version of tracula require the b0 entries to be removed? If not, any suggestions on what I may be doing incorrectly would be great. Thank you. Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] longitudinal hippocampal subfields analysis
Hi, I have been able to do the longitudinal processing steps for a number of subjects with 3 time points each, and then extract the generated statistics using aparcstats2table and asegstats2table. Is it possible to perform longitudinal analysis of the hippocampal subfields? If so, could someone point me to how to perform this analysis, as kvlQuantifyHippocampalSubfieldSegmentations.sh does not work on the output files I've generated. Thank you. Salil Soman, MD, MS ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] longitudinal hippocampal subfields analysis
Thank you Martin. I will try this approach. I was able to temporarily move the longitudinal subject data to its own folder to run aparc2table and aseg2table. Hopefully this will also work for the hippocampal subfield script. Best wishes, Sal Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System On Jan 7, 2014 8:07 AM, "Martin Reuter" wrote: > Hi Salil, > > just run the hippo-subfields on the longitudinal results like this: > > recon-all -long -hippo-subfields > > to generate the subfield data. I am not familiar with the kvlQuantify... > script and think it works on all subjects in the Subjects dir. Not sure > what the best way is to solve this as your subject dir contains also the > cross and base results. Probably you can run the script and it will simply > skip the cross and base directories (as no -hippo-subfields was run on > them). > > > Best, Martin > > > On 01/05/2014 01:40 AM, Salil Soman wrote: > > Hi, > > I have been able to do the longitudinal processing steps for a number of > subjects with 3 time points each, and then extract the generated statistics > using aparcstats2table and asegstats2table. Is it possible to perform > longitudinal analysis of the hippocampal subfields? If so, could someone > point me to how to perform this analysis, > as kvlQuantifyHippocampalSubfieldSegmentations.sh does not work on the > output files I've generated. > > Thank you. > > Salil Soman, MD, MS > > > ___ > Freesurfer mailing > listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > -- > Martin Reuter, Ph.D. > Assistant in Neuroscience - Massachusetts General Hospital > Instructor in Neurology - Harvard Medical School > MGH / HMS / MIT > > A.A.Martinos Center for Biomedical Imaging > 149 Thirteenth Street, Suite 2301 > Charlestown, MA 02129 > > Phone: +1-617-724-5652 > Email: >mreu...@nmr.mgh.harvard.edu >reu...@mit.edu > Web : http://reuter.mit.edu > > The information in this e-mail is intended only for the person to whom > it is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] problem with bvecs file with new (12/13) TRACULA code
Hi, I am re-running GE acquired 3T product DTI data which ran without trouble through the older tracula code. However, now when I run the code, the bvec file that gets generated has an extra 0 placed at the very end, and then trac-all -prep eventually fails because it complains the bvec and bvals files have non-matching number of entries. I do have the dorotbvecs option set to 1 (as I had before). Any suggestions on what I am doing incorrectly would be greatly appreciated. I have attached the bvec and bval files I am providing a input. Best wishes, Sal -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System AxDTI1.bvec Description: Binary data AxDTI1.bval Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Fwd: Re: problem with bvecs file with new (12/13) TRACULA code
-- Forwarded message -- From: "Salil Soman" Date: Jan 12, 2014 1:28 PM Subject: Re: problem with bvecs file with new (12/13) TRACULA code To: "Anastasia Yendiki" Cc: Hi, > > Thank you for your email. Taking the .bval and bvec files outputed by > dcm2nii (which are row format) and transposing them to column format was > resulting in the blank rows that were causing troubles. Running this > command got rid of the problems and allowed trac-all prep / bedp / and path > to complete without errors: > > sed '/^\s*$/d' > > > Thanks, > > Sal > > > On Fri, Jan 10, 2014 at 3:57 PM, Anastasia Yendiki < > ayend...@nmr.mgh.harvard.edu> wrote: > >> >> Hi Sal - It looks like a problem with the spaces at the end of the lines >> of the bvecs file. If you remove those spaces, it should work. Thanks for >> bringing this to my attention - the row-formatted bvecs files are new in >> this version and I'll make sure to allow them to have spaces at the end of >> the lines in the future. >> >> a.y >> >> >> On Thu, 9 Jan 2014, Salil Soman wrote: >> >> Hi, >>> >>> I am re-running GE acquired 3T product DTI data which ran without >>> trouble through the older tracula code. >>> However, now when I run the code, the bvec file that gets generated has >>> an extra 0 placed at the very end, >>> and then trac-all -prep eventually fails because it complains the bvec >>> and bvals files have non-matching >>> number of entries. I do have the dorotbvecs option set to 1 (as I had >>> before). Any suggestions on what I am >>> doing incorrectly would be greatly appreciated. I have attached the bvec >>> and bval files I am providing a >>> input. >>> >>> Best wishes, >>> >>> Sal >>> -- >>> Salil Soman, MD, MS >>> Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory >>> Fellow - Palo Alto War Related Illness and Injury Study Center >>> WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care >>> System >>> >>> >>> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> > > > > -- > Salil Soman, MD, MS > Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory > Fellow - Palo Alto War Related Illness and Injury Study Center > WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care > System > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Tracula only outputs merged flt file (and missing bbr)
Hi, Is there a specific issue to troubleshoot if Tracula only creates the merged ... flt file and not the merged ... bbr file in paths? All of my dmrirc files have both bbr and flt =1, and most of my outputs have both, but occasionally I only get 1. Thanks! -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Outputting all tracula statistics to table
Hi, What is the proper way to generate a single table containing all tracula generated statistics for all subjects in a study? I tought tractstats2table was the way to do this, I am confused as to how trac-all -stat factors into this process in the latest (12-09-13 version)? Thank you. -Sal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Tracula shows some tracks with bbr and others with flt
Hi, I have a couple of dti cases where bbr will include forceps major and missing forceps minor and flt will be the opposite. Similar things have occurred for anterior thalamic tracts and cingulum bundles. Any suggestions on what I may be doing incorrectly? Best wishes, Sal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Tracula only outputs merged flt file (and missing bbr)
This had only occurred for 1 case lot of the last 100. I will look into your suggestions. Thank you. Sal On Feb 5, 2014 4:48 PM, "Anastasia Yendiki" wrote: > > Hi Sal - That sounds strange. Are the individual paths created normally > for the bbr case? So there are subdirectories with path.pd.nii.gz files for > all the tracts? Does the trac-all.log show any commands run or error > messages for the bbr case? > > a.y > > On Sat, 18 Jan 2014, Salil Soman wrote: > > Hi, >> Is there a specific issue to troubleshoot if Tracula only creates the >> merged ... flt >> file and not the merged ... bbr file in paths? All of my dmrirc files >> have both bbr and >> flt =1, and most of my outputs have both, but occasionally I only get 1. >> >> Thanks! >> >> >> -- >> Salil Soman, MD, MS >> Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory >> Fellow - Palo Alto War Related Illness and Injury Study Center >> WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care >> System >> >> >> > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] possible to render hippocampal subfield segmentations as 3D structures?
Hi, I generated hippocampal subfield segmentations, can generate statistics, but was wondering if there was a way to visualized the subfield segmentations as a 3D structure? (e.g. like the figure in this paper: http://niacal.northwestern.edu/projects/17) Thank you for your consideration. Best wishes, -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] possible to render hippocampal subfield segmentations as 3D structures?
Thank you for your email. I have been using the command: freeview nu.mgz -p-labels posterior_left_* posterior_Left-Hippocampus.mgz -p-labels posterior_right_* posterior_Right-Hippocampus.mgz -p-prefix posterior_ -p-lut $FREESURFER_HOME/FreeSurferColorLUT.txt to visualize the hippocampal subfield segmentations. However this created the posterior_ entries, which when I turn on the isosurface view, makes a solid structure, which I can adjust the color. But when I try to load in the individual volumes (e.g. posterior_right_CA2_3.mgz) I get a separate structure that is not at all registered with the right hippocampus. Any suggestions on what I am doing incorrectly? -S On Thu, Feb 6, 2014 at 10:38 AM, Louis Nicholas Vinke < vi...@nmr.mgh.harvard.edu> wrote: > Hi Salil, > You should be able to apply an isosurface to each subfield label in > freeview. You can set the color for each isosurface as well, since the > default is gray. You need to be in the 3D view in order to display > isosurfaces. > -Louis > > > On Thu, 6 Feb 2014, Salil Soman wrote: > > Hi, >> I generated hippocampal subfield segmentations, can generate statistics, >> but >> was wondering if there was a way to visualized the subfield segmentations >> as >> a 3D structure? (e.g. like the figure in this >> paper: http://niacal.northwestern.edu/projects/17) >> >> Thank you for your consideration. >> >> Best wishes, >> >> -- >> Salil Soman, MD, MS >> Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory >> Fellow - Palo Alto War Related Illness and Injury Study Center >> WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care >> System >> >> >> > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] possible to do multi planar reformats of hippocampal subfields in freeview?
Hi, I am reviewing hippocampal subfield segmentation using freeview, and was wondering if there is a way to do multiplanar reformats so I can get reorient the cor/sag/axial planes to that of the hippocampus? Thank you. -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] possible to see an example of phase map input for tracula?
Hi, Could someone point me to an example for a sample phase map that tracula can take as input? We do not have a specific sequence for this on our GE system but may be able to output it from some of our 3D GRE sequences. Best wishes, -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] What coordinate space is freesurfer output in?
Hi, I was wondering what the default freesurfer coordinate space is called? (MNI, something else)? Thanks, Sal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] bbr problem run
Here are the errors from the trac-all.log file I sent earlier: mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/Test_FS/mri/ERROR: /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dmri/xfms/tmp.bbregister.23392/fslregister/refvol.fslregister.nii mri_convert ERROR: could not determine file for /mnt/glusterfs/salsoman/output/FS/Test_FS/mri/ERROR: /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dmri/xfms/tmp.bbregister.23392/fslregister/refvol.fslregister.nii ** ERROR (nifti_image_read): failed to find header file for '/mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dmri/xfms/tmp.bbregister.23392/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(/mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dmri/xfms/tmp.bbregister.23392/fslregister/refvol.fslregister): bad header info ERROR: failed to open file /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dmri/xfms/tmp.bbregister.23392/fslregister/refvol.fslregister ERROR: Could not open image /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dmri/xfms/tmp.bbregister.23392/fslregister/refvol.fslregister ** ERROR (nifti_image_read): failed to find header file for '/mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dmri/xfms/tmp.bbregister.23392/fslregister/refvol.fslregister' ** ERROR: nifti_image_open(/mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dmri/xfms/tmp.bbregister.23392/fslregister/refvol.fslregister): bad header info ERROR: failed to open file /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dmri/xfms/tmp.bbregister.23392/fslregister/refvol.fslregister ERROR: Could not open image /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dmri/xfms/tmp.bbregister.23392/fslregister/refvol.fslregister ERROR: cannot open /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dmri/xfms/tmp.bbregister.23392/reg.init.dat.fsl.mat ERROR: reading /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dmri/xfms/anatorig2diff.bbr.dat Image Exception : #22 :: ERROR: Could not open image /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/diff/White-Matter++.flt ERROR: Could not open /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dmri/xfms/mni2diff.bbr.mat ERROR: Could not read /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz ERROR: Could not read /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz On Thu, Mar 28, 2013 at 4:22 PM, Salil Soman wrote: > Thank you for your response. > > I tried re-running Tracula using bbr in a subject I had successfully run > using flt. trac-all prep and bedp worked without an error. Bedpostx sent me > an email confirming bedpost completed without problem. However, when I try > to run trac-all paths, I get the following error: > > Loading atlas reference volume from > /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.$ > niiRead(): error opening file > /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz > ERROR: Could not read > /mnt/glusterfs/salsoman/output/TRACULA/Test_FS/dlabel/mni/lh.cst_AS_avg33_mni_bbr_end1_dil.nii.gz > > recon-all did finish without error. > > Best wishes, > > -S > > > On Thu, Mar 28, 2013 at 8:43 AM, Anastasia Yendiki < > ayend...@nmr.mgh.harvard.edu> wrote: > >> >> Hi Sal, >> >> 1. I have no experience with the sun grid engine, perhaps someone else on >>the list can help with that. >> >> 2. The -bedp step needs the outputs from the -corr and -masks steps. The >>-path step needs the outputs from the -bedp step. The output files from >>each part are listed here: >>http://www.freesurfer.net/**fswiki/trac-all#** >> Outputdirectoriesandfiles<http://www.freesurfer.net/fswiki/trac-all#Outputdirectoriesandfiles> >> >> 3. Checking the aparc+aseg should be enough for tracula purposes as well, >>since that's the freesurfer output that tracula uses. Keep in mind that >>DWI resolution is usually lower than T1 resolution, so tiny changes in >>the aparc+aseg might not affect tracula at all. >> >> 4. Yes, I do recommend using bbregister. It's not surprising that it would >>give better results since it uses the additional information of the >>surfaces. If I remember correctly, Doug didn't manage to replicate your >>bbregister error, right? I'd check if you get the same error with the >>5.1 version of bbregister. >> >> Hope this helps, >> a.y >> >> >> On Wed, 27 Mar 2013, Salil Soman wrote: >> >> Hi, >>> I have been able to implement FS 5.2 on our Sun Grid Engine Cluster >>> using the CentOS 6 >>> distribution. After modifying the fsl_sub_mgh file to work with ou
[Freesurfer] FS 5.2 asegstats2table is not found or is too small to be a valid stats file error
Dear Experts, I am trying to extract FS 5.2 statistics for a single subject using the following command: asegstats2table --subjects SUBJECTNAME --tablefile teststats.txt I keep getting *the following error: * *The stats file /PATH/SUBJECTNAME/stats/aseg.stats is not found or is too small to be a valid statsfile Use --skip flag to automatically skip bad stats files * Any suggestions on what I am doing incorrectly? I would like to extract all of the statistics in aseg.stats into a single row per subject to facilitate additional analysis in other programs. Any suggestions on how to accomplish this would be much appreciated. Thank you. -S* * ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] recon-all with multiple spgr's per subject
Dear Freesurfer experts, Could someone point me to the syntax for having recon-all use multiple T1 volumes for the same subject (which I believe it is supposed to motion correct and average). Thanks, Salil Soman, MD, MS ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences
Thank you Doug. Just so I am clear - is the anatomical the nifti T1.mgz or is it a different file. From your email I gather should do the following: *1) Use bbregister to register the lowb image to the anatomical. This creates a registration matrix.* bbregister -s SUBJECTNAME --mov lowb.nii --initfsl --reg register.dat *2) Use mri_vol2vol and the registration to map the ADC map to the anatomical* mri_vol2vol --mov lowb.nii --targ $vol --inv --interp nearest --o $vol2diff --reg $outdir/register.dat --no-save-reg *3) use mri_segstats to extract the values* *mri_segstats* --seg $SUBJECTS_DIR/SUBJECTNAME/mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i lowb.nii --sum fa.stats Where lowb.nii is the other MRI tissue sequence I am analyzing (e.g. ADC), $vol2diff is the output image of the registration, and fa.stats will be my output stats table? I suspect there is part of the syntax for these tools I do not understand. Also, what input would $vol be? Best wishes, Sal On Sat, May 25, 2013 at 10:06 AM, Douglas Greve wrote: > > Hi Sal, yes you can. Use bbregister to register the lowb image to the > anatomical. This creates a registration matrix. Use mri_vol2vol and the > registration to map the ADC map to the anatomical, then use mri_segstats to > extract the values > doug > > ps. Please post questions to the FS list instead of us directly so that > others can benefit and it gets archived. thanks! > > > > On 5/25/13 1:03 PM, Salil Soman wrote: > >> Dear Dr. Greve, >> >> Is it possible to register a nonstructural MR sequences (e.g. an ADC map) >> with the aseg.mgz file (or aparc+aseg.mgz file, etc) and then, using the >> segmentation from the aseg (or aparc+aseg) file to output a mean ADC value >> for each anatomic area segmented? >> >> Thank you for your time and consideration. >> >> Best wishes, >> >> Sal >> >> Salil Soman, MD, MS >> > > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. > If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Fwd: BBR Register failing
-- Forwarded message --
From: Salil Soman
Date: Sat, May 25, 2013 at 8:00 PM
Subject: BBR Register failing
To: Douglas N Greve
Dear Doug,
I attempted to run the process we discussed earlier today for registering a
different tissue contrast to the T1 after freesurfer 5.3 was run.
I had run an FSSPGR for my subject using the following command:
recon-all -i SPGR/*.gz -s WMR3T_0015z_FS -nuintensitycor-3T -nocanorm
-openmp 50 -hippo-subfields -all
It finished without any problems.
Then I tried running the bbrregister command:
bbregister --s WMR3T_0015z_FS --mov QSM_906.nii.gz --init-fsl --reg
register.dat --bold
(this version was with bold contrast, but I get the same error if I try t1
or t2).
The process fails and I get the following error log (below). Any
suggestions on what I am doing wrong?
Thanks,
Sal
-- Forwarded message --
From: Salil Soman
Date: Sat, May 25, 2013 at 7:54 PM
Subject: bbregister fail log
To: salso...@stanford.edu
Logfile for bbregister
Sat May 25 19:51:15 PDT 2013
setenv SUBJECTS_DIR /mnt/glusterfs/salsoman/output/FS
cd /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS
/mnt/glusterfs/salsoman/freesurfer/bin/bbregister --s WMR3T_0015z_FS --mov
QSM_906.nii.gz --init-fsl --reg register.dat --bold
$Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $
Linux corn18.stanford.edu 3.2.0-36-generic #57-Ubuntu SMP Tue Jan 8
21:44:52 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
FREESURFER_HOME /mnt/glusterfs/salsoman/freesurfer
mri_convert QSM_906.nii.gz ./tmp.bbregister.26724/template.nii
mri_convert QSM_906.nii.gz ./tmp.bbregister.26724/template.nii
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from QSM_906.nii.gz...
TR=98.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0.313177, 0.949695)
k_ras = (0, -0.949695, 0.313177)
writing to ./tmp.bbregister.26724/template.nii...
fslregister --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/template.nii
--reg ./tmp.bbregister.26724/reg.init.dat --niters 1 --maxangle 90
--nobetmov --tmp ./tmp.bbregister.26724/fslregister --dof 6 --fsvol
brainmask
Log file is ./tmp.bbregister.26724/reg.init.dat.fslregister.log
Sat May 25 19:51:17 PDT 2013
--s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/template.nii --reg
./tmp.bbregister.26724/reg.init.dat --niters 1 --maxangle 90 --nobetmov
--tmp ./tmp.bbregister.26724/fslregister --dof 6 --fsvol brainmask
$Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $
corn18.stanford.edu
Linux corn18.stanford.edu 3.2.0-36-generic #57-Ubuntu SMP Tue Jan 8
21:44:52 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
nIters 1
--
/mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS
mri_convert ERROR: could not determine file for
/mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR:
./tmp.bbregister.26724/fslregister/refvol.fslregister.nii
mri_convert ERROR: could not determine file for
/mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR:
./tmp.bbregister.26724/fslregister/refvol.fslregister.nii
mri_convert: extra arguments ("not" and following)
type mri_convert -u for usage
--
/mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS
mri_convert ./tmp.bbregister.26724/template.nii
./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --frame 0
mri_convert ./tmp.bbregister.26724/template.nii
./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --frame 0
$Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
reading from ./tmp.bbregister.26724/template.nii...
TR=98.00, TE=0.00, TI=0.00, flip angle=0.00
i_ras = (-1, 0, 0)
j_ras = (0, 0.313177, 0.949695)
k_ras = (0, -0.949695, 0.313177)
keeping frame 0
writing to ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii...
Mov determinant is -0.984886
/mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS
tkregister2_cmdl --mov
./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --reg
./tmp.bbregister.26724/fslregister/reg0.26760.dat --regheader --fslregout
./tmp.bbregister.26724/reg.init.dat.fsl.mat0 --s WMR3T_0015z_FS --noedit
tkregister_tcl /mnt/glusterfs/salsoman/freesurfer/tktools/tkregister2.tcl
INFO: no target volume specified, assuming FreeSurfer orig volume.
target volume orig
movable volume ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii
reg file ./tmp.bbregister.26724/fslregister/reg0.26760.dat
LoadVol0
ZeroCRAS 0
$Id: tkregister2.c,v 1.121.2.1 2011/03/28 20:25:16 greve Exp $
Diagnostic Level -1
INFO: loading target
/mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/orig.mgz
Ttarg:
-1.000 0.000 0.000 128.000;
0.000 0.000 1.000 -128.000;
0.000 -1.000 0.000 128.000;
0.000 0.000 0.000 1.000;
INFO: loading movable
./tmp.bbregister.26724/fslregister/movvol.fslregister.nii
Tmov:
-1.000 0.000 0.000 112.000;
0.000 0.000 0.985 -83.715;
0.000 -1.000 0.000 112.000;
0.000 0.0
Re: [Freesurfer] BBR Register failing
Done. Thank you for your consideration. The best I can figure so far is
1) the script's attempt to make the tmp.bbregister.7392 directory fails
and 2) (after I manually make this directory),
there seems to be something going wrong at the level of fslregister
I have fsl 5.0.2.1 and freesurfer 5.3 running, and am regularly able to run
freesurfer and
tracula (using only the flirt method, the bbr method was giving me trouble
as well).
The code is all running on a sun grid engine, with individual ubuntu
12.04.1 LTS machines.
Your help on this matter would be greatly appreciated.
Sal
On Sat, May 25, 2013 at 8:23 PM, Douglas Greve wrote:
> Hi Sal, can you post this to the list instead of me directly?
> thanks!
> doug
>
>
>
> On 5/25/13 11:00 PM, Salil Soman wrote:
>
>Dear Doug,
>
> I attempted to run the process we discussed earlier today for registering
> a different tissue contrast to the T1 after freesurfer 5.3 was run.
>
> I had run an FSSPGR for my subject using the following command:
>
> recon-all -i SPGR/*.gz -s WMR3T_0015z_FS -nuintensitycor-3T -nocanorm
> -openmp 50 -hippo-subfields -all
>
> It finished without any problems.
>
> Then I tried running the bbrregister command:
>
> bbregister --s WMR3T_0015z_FS --mov QSM_906.nii.gz --init-fsl --reg
> register.dat --bold
>
> (this version was with bold contrast, but I get the same error if I try
> t1 or t2).
>
> The process fails and I get the following error log (below). Any
> suggestions on what I am doing wrong?
>
> Thanks,
>
> Sal
>
> -- Forwarded message --
> From: Salil Soman
> Date: Sat, May 25, 2013 at 7:54 PM
> Subject: bbregister fail log
> To: salso...@stanford.edu
>
>
> Logfile for bbregister
> Sat May 25 19:51:15 PDT 2013
>
> setenv SUBJECTS_DIR /mnt/glusterfs/salsoman/output/FS
> cd /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS
> /mnt/glusterfs/salsoman/freesurfer/bin/bbregister --s WMR3T_0015z_FS --mov
> QSM_906.nii.gz --init-fsl --reg register.dat --bold
>
> $Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $
> Linux corn18.stanford.edu 3.2.0-36-generic #57-Ubuntu SMP Tue Jan 8
> 21:44:52 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
> FREESURFER_HOME /mnt/glusterfs/salsoman/freesurfer
> mri_convert QSM_906.nii.gz ./tmp.bbregister.26724/template.nii
> mri_convert QSM_906.nii.gz ./tmp.bbregister.26724/template.nii
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from QSM_906.nii.gz...
> TR=98.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-1, 0, 0)
> j_ras = (0, 0.313177, 0.949695)
> k_ras = (0, -0.949695, 0.313177)
> writing to ./tmp.bbregister.26724/template.nii...
> fslregister --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/template.nii
> --reg ./tmp.bbregister.26724/reg.init.dat --niters 1 --maxangle 90
> --nobetmov --tmp ./tmp.bbregister.26724/fslregister --dof 6 --fsvol
> brainmask
>
> Log file is ./tmp.bbregister.26724/reg.init.dat.fslregister.log
>
> Sat May 25 19:51:17 PDT 2013
> --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/template.nii --reg
> ./tmp.bbregister.26724/reg.init.dat --niters 1 --maxangle 90 --nobetmov
> --tmp ./tmp.bbregister.26724/fslregister --dof 6 --fsvol brainmask
> $Id: fslregister,v 1.34.2.2 2012/11/08 16:18:56 greve Exp $
> corn18.stanford.edu
> Linux corn18.stanford.edu 3.2.0-36-generic #57-Ubuntu SMP Tue Jan 8
> 21:44:52 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
> nIters 1
> --
> /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS
> mri_convert ERROR: could not determine file for
> /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR:
> ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii
> mri_convert ERROR: could not determine file for
> /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR:
> ./tmp.bbregister.26724/fslregister/refvol.fslregister.nii
>
> mri_convert: extra arguments ("not" and following)
>
> type mri_convert -u for usage
>
> --
> /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS
> mri_convert ./tmp.bbregister.26724/template.nii
> ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --frame 0
> mri_convert ./tmp.bbregister.26724/template.nii
> ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii --frame 0
> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
> reading from ./tmp.bbregister.26724/template.nii...
> TR=98.00, TE=0.00, TI=0.00, flip angle=0.00
> i_ras = (-1, 0, 0)
> j_ras = (0, 0.313177, 0.949695)
> k_ras = (0, -0.949695, 0.313177)
> keeping frame 0
> writing to ./tmp.bbregister.26724/fslregister/movvol.fslregister.nii...
> Mov determinant is -0.984886
> /mnt/gluste
Re: [Freesurfer] BBR Register failing
Dear Freesurfer experts,
WIth the combination of FS 5.3 and FSL 5.0.2.1, It looks like I am having
some problems with the fslregister script. From what I have been able to
investigate. It looks like there is an issue that fsvol may not get named
if you are not dealing .cor files.
Code in question from fslregister script:
# Use the rawavg as input (for testing only)
if($fsvol == rawavg.cor) then
set refvol = $SUBJECTS_DIR/$subjid/mri/$fsvol.mgz
if(! -e $refvol) then
# Does not exist, create
set orig = $SUBJECTS_DIR/$subjid/mri/orig.mgz
set rawavg = $SUBJECTS_DIR/$subjid/mri/rawavg.mgz
set cmd = (mri_vol2vol --mov $rawavg --targ $orig --o $refvol \
--no-save-reg --regheader)
echo $cmd |& tee -a $LF
$cmd |& tee -a $LF
if($status) exit 1;
# Now mask it
set brain = $SUBJECTS_DIR/$subjid/mri/brainmask.mgz
set cmd = (mri_mask $refvol $brain $refvol)
echo $cmd |& tee -a $LF
$cmd |& tee -a $LF
I think this lack of fsvol being named results in the errors I am getting:
--
/mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS
mri_convert ERROR: could not determine file for
/mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR:
./tmp.bbregister.756/fslregister/refvol.fslregister.nii
mri_convert ERROR: could not determine file for
/mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS/mri/ERROR:
./tmp.bbregister.756/fslregister/refvol.fslregister.nii
mri_convert: extra arguments ("not" and following)
Any suggestions would be a huge help.
-Sal
On Sat, May 25, 2013 at 8:35 PM, Salil Soman wrote:
> Done. Thank you for your consideration. The best I can figure so far is
> 1) the script's attempt to make the tmp.bbregister.7392 directory fails
> and 2) (after I manually make this directory),
> there seems to be something going wrong at the level of fslregister
>
> I have fsl 5.0.2.1 and freesurfer 5.3 running, and am regularly able to
> run freesurfer and
> tracula (using only the flirt method, the bbr method was giving me trouble
> as well).
>
> The code is all running on a sun grid engine, with individual ubuntu
> 12.04.1 LTS machines.
>
> Your help on this matter would be greatly appreciated.
>
> Sal
>
>
>
> On Sat, May 25, 2013 at 8:23 PM, Douglas Greve
> wrote:
>
>> Hi Sal, can you post this to the list instead of me directly?
>> thanks!
>> doug
>>
>>
>>
>> On 5/25/13 11:00 PM, Salil Soman wrote:
>>
>>Dear Doug,
>>
>> I attempted to run the process we discussed earlier today for
>> registering a different tissue contrast to the T1 after freesurfer 5.3 was
>> run.
>>
>> I had run an FSSPGR for my subject using the following command:
>>
>> recon-all -i SPGR/*.gz -s WMR3T_0015z_FS -nuintensitycor-3T -nocanorm
>> -openmp 50 -hippo-subfields -all
>>
>> It finished without any problems.
>>
>> Then I tried running the bbrregister command:
>>
>> bbregister --s WMR3T_0015z_FS --mov QSM_906.nii.gz --init-fsl --reg
>> register.dat --bold
>>
>> (this version was with bold contrast, but I get the same error if I try
>> t1 or t2).
>>
>> The process fails and I get the following error log (below). Any
>> suggestions on what I am doing wrong?
>>
>> Thanks,
>>
>> Sal
>>
>> -- Forwarded message --
>> From: Salil Soman
>> Date: Sat, May 25, 2013 at 7:54 PM
>> Subject: bbregister fail log
>> To: salso...@stanford.edu
>>
>>
>> Logfile for bbregister
>> Sat May 25 19:51:15 PDT 2013
>>
>> setenv SUBJECTS_DIR /mnt/glusterfs/salsoman/output/FS
>> cd /mnt/glusterfs/salsoman/output/FS/WMR3T_0015z_FS
>> /mnt/glusterfs/salsoman/freesurfer/bin/bbregister --s WMR3T_0015z_FS
>> --mov QSM_906.nii.gz --init-fsl --reg register.dat --bold
>>
>> $Id: bbregister,v 1.49.2.2 2013/02/23 01:32:22 mreuter Exp $
>> Linux corn18.stanford.edu 3.2.0-36-generic #57-Ubuntu SMP Tue Jan 8
>> 21:44:52 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux
>> FREESURFER_HOME /mnt/glusterfs/salsoman/freesurfer
>> mri_convert QSM_906.nii.gz ./tmp.bbregister.26724/template.nii
>> mri_convert QSM_906.nii.gz ./tmp.bbregister.26724/template.nii
>> $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $
>> reading from QSM_906.nii.gz...
>> TR=98.00, TE=0.00, TI=0.00, flip angle=0.00
>> i_ras = (-1, 0, 0)
>> j_ras = (0, 0.313177, 0.949695)
>> k_ras = (0, -0.949695, 0.313177)
>> writing to ./tmp.bbregister.26724/template.nii...
>> fslregister --s WMR3T_0015z_FS --mov ./tmp.bbregister.26724/template.nii
>> --reg ./tmp.bbregister.26724/reg.init.dat --niters 1 --maxangle
Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences
Dear Doug, Thank you for your email. Following up on our previous discussions: 1) *bbregister fail *- this was happening because of error from fslregister. The variable fsvol was translating to "ERROR". In fslregister th value for fsvol is set to brainmask, along with numerous other parameters being initialized. By adding the line "set fsvol = brain mask" (without quotes) at the beginning of the section "#Convert reference to analyze" the CentOS 6 version I am running on ubuntu 12.04 (with SGE), now works. 2) when you suggested I run bbregister on the lowb.nii file, was it because I had suggested I wanted to register to a 2D ADC map? If I want to instead use a 3D volume (e.g. a 3D ASL), would I use the actual volume I want to get value from instead of lowb.nii? I ended up running 3) for the mri_vol2vol step - I had to change targ to fstarg, and I left out the interp flag so it would do its default trilinear: mri_vol2vol --mov Vol_906.nii --fstarg T1.mgz --o Vol_906_Reg_Bold.nii --no-save-reg --reg register_bold.dat --inv 4) I would like to get the segmentations from aparc+aseg.mgz as the areas where I get the values summed. So I entered mri_segstats --seg mri/aparc+aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i Vol_906_Reg_Bold.nii --sum Vol_aparc_aseg.stats but then I received this error: ERROR: dimension mismatch between input volume and seg input 224 224 170 seg 256 256 256 * * *So, in summary, while I've fixed bbregister to work on my system, I am still having trouble normalizing my 3D non T1 volume data into the FS space to be able to use the labels from aparc+aseg.mgz to get statistics for each anatomic area.* Any ideas on how to proceed? Thanks, Sal On Sat, May 25, 2013 at 11:51 AM, Douglas Greve wrote: > > On 5/25/13 1:39 PM, Salil Soman wrote: > > Thank you Doug. > > Just so I am clear - is the anatomical the nifti T1.mgz or is it a > different file. From your email I gather should do the following: > > *1) Use bbregister to register the lowb image to the anatomical. This > creates a registration matrix.* > > bbregister -s SUBJECTNAME --mov lowb.nii --initfsl --reg register.dat > > That is right, but add --t2 (since it is t2 weighted). > > > *2) Use mri_vol2vol and the registration to map the ADC map to the > anatomical* > > mri_vol2vol --mov lowb.nii --targ $vol --inv --interp nearest --o $vol2diff > --reg $outdir/register.dat --no-save-reg > > Use the ADC as the moveable (not lowb, but use the lowb for > bbregister). The target volume should be the T1.mgz (or any conformed > volume). The output will be the adc in the anatomical space (not sure why > you call it vol2diff). > >*3) use mri_segstats to extract the values* > > *mri_segstats* --seg $SUBJECTS_DIR/SUBJECTNAME/mri/wmparc.mgz --ctab > $FREESURFER_HOME/FreeSurferColorLUT.txt --i lowb.nii --sum fa.stats > > The input would be the adc volume mapped the anatomical space. I would > use WMParcStatsLUT.txt or else you'll get a billion different areas not > represented in wmparc. You may also want to add "--seg-erode 1" to erode > the segmentations by a voxel. This helps to prevent partial voluming. > > doug > > > > Where lowb.nii is the other MRI tissue sequence I am analyzing (e.g. > ADC), $vol2diff is the output image of the registration, and fa.stats will > be my output stats table? > > I suspect there is part of the syntax for these tools I do not > understand. Also, what input would $vol be? > > Best wishes, > > Sal > > > On Sat, May 25, 2013 at 10:06 AM, Douglas Greve > wrote: > >> >> Hi Sal, yes you can. Use bbregister to register the lowb image to the >> anatomical. This creates a registration matrix. Use mri_vol2vol and the >> registration to map the ADC map to the anatomical, then use mri_segstats to >> extract the values >> doug >> >> ps. Please post questions to the FS list instead of us directly so that >> others can benefit and it gets archived. thanks! >> >> >> >> On 5/25/13 1:03 PM, Salil Soman wrote: >> >>> Dear Dr. Greve, >>> >>> Is it possible to register a nonstructural MR sequences (e.g. an ADC >>> map) with the aseg.mgz file (or aparc+aseg.mgz file, etc) and then, using >>> the segmentation from the aseg (or aparc+aseg) file to output a mean ADC >>> value for each anatomic area segmented? >>> >>> Thank you for your time and consideration. >>> >>> Best wishes, >>> >>> Sal >>> >>> Salil Soman, MD, MS >>> >> >> >> >> The information in this e-mail is intended only for the person to whom >> it is >> addres
Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences
Hi - I realize that the --inv tag was still in my commands for mr_vol2vol (causing the target and the moving image to be swapped). Removing the --inv tag gave me a new volume normalized to aparc+aseg.nii, and so I was able to then run mri_segstats using the following command: mri_segstats --seg mri/aparc+aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i Vol_906_Reg_Bold.nii --sum Vol_906_aparc_aseg.stats Thanks! -S On Sun, May 26, 2013 at 11:11 AM, Salil Soman wrote: > Dear Doug, > > Thank you for your email. Following up on our previous discussions: > > 1) *bbregister fail *- this was happening because of error from > fslregister. The variable fsvol was translating to "ERROR". In fslregister > th value for fsvol is set to brainmask, along with numerous other > parameters being initialized. > By adding the line "set fsvol = brain mask" (without quotes) at the > beginning of the section "#Convert reference to analyze" the CentOS 6 > version I am running on ubuntu 12.04 (with SGE), now works. > > 2) when you suggested I run bbregister on the lowb.nii file, was it > because I had suggested I wanted to register to a 2D ADC map? If I want to > instead use a 3D volume (e.g. a 3D ASL), would I use the actual volume I > want to get value from instead of lowb.nii? I ended up running > > 3) for the mri_vol2vol step - I had to change targ to fstarg, and I left > out the interp flag so it would do its default trilinear: mri_vol2vol > --mov Vol_906.nii --fstarg T1.mgz --o Vol_906_Reg_Bold.nii --no-save-reg > --reg register_bold.dat --inv > > 4) I would like to get the segmentations from aparc+aseg.mgz as the areas > where I get the values summed. So I entered mri_segstats --seg > mri/aparc+aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i > Vol_906_Reg_Bold.nii --sum Vol_aparc_aseg.stats > > but then I received this error: > > ERROR: dimension mismatch between input volume and seg > input 224 224 170 > seg 256 256 256 > * > * > *So, in summary, while I've fixed bbregister to work on my system, I am > still having trouble normalizing my 3D non T1 volume data into the FS space > to be able to use the labels from aparc+aseg.mgz to get statistics for each > anatomic area.* > > Any ideas on how to proceed? > > Thanks, > > Sal > > > On Sat, May 25, 2013 at 11:51 AM, Douglas Greve > wrote: > >> >> On 5/25/13 1:39 PM, Salil Soman wrote: >> >> Thank you Doug. >> >> Just so I am clear - is the anatomical the nifti T1.mgz or is it a >> different file. From your email I gather should do the following: >> >> *1) Use bbregister to register the lowb image to the anatomical. This >> creates a registration matrix.* >> >> bbregister -s SUBJECTNAME --mov lowb.nii --initfsl --reg register.dat >> >> That is right, but add --t2 (since it is t2 weighted). >> >> >> *2) Use mri_vol2vol and the registration to map the ADC map to the >> anatomical* >> >> mri_vol2vol --mov lowb.nii --targ $vol --inv --interp nearest --o $vol2diff >> --reg $outdir/register.dat --no-save-reg >> >> Use the ADC as the moveable (not lowb, but use the lowb for >> bbregister). The target volume should be the T1.mgz (or any conformed >> volume). The output will be the adc in the anatomical space (not sure why >> you call it vol2diff). >> >>*3) use mri_segstats to extract the values* >> >> *mri_segstats* --seg $SUBJECTS_DIR/SUBJECTNAME/mri/wmparc.mgz --ctab >> $FREESURFER_HOME/FreeSurferColorLUT.txt --i lowb.nii --sum fa.stats >> >> The input would be the adc volume mapped the anatomical space. I would >> use WMParcStatsLUT.txt or else you'll get a billion different areas not >> represented in wmparc. You may also want to add "--seg-erode 1" to erode >> the segmentations by a voxel. This helps to prevent partial voluming. >> >> doug >> >> >> >> Where lowb.nii is the other MRI tissue sequence I am analyzing (e.g. >> ADC), $vol2diff is the output image of the registration, and fa.stats will >> be my output stats table? >> >> I suspect there is part of the syntax for these tools I do not >> understand. Also, what input would $vol be? >> >> Best wishes, >> >> Sal >> >> >> On Sat, May 25, 2013 at 10:06 AM, Douglas Greve < >> gr...@nmr.mgh.harvard.edu> wrote: >> >>> >>> Hi Sal, yes you can. Use bbregister to register the lowb image to the >>> anatomical. This creates a registration matrix. Use mri_vol2vol and the >>> registration to map the A
Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences
As I am working with a 3D volume and not an ADC map, should I still use --seg-erode 1 with mr segstats? Thank On Sun, May 26, 2013 at 1:11 PM, Salil Soman wrote: > Hi - I realize that the --inv tag was still in my commands for mr_vol2vol > (causing the target and the moving image to be swapped). Removing the --inv > tag gave me a new volume normalized to aparc+aseg.nii, and so I was able to > then run mri_segstats using the following command: > > mri_segstats --seg mri/aparc+aseg.mgz --ctab > $FREESURFER_HOME/FreeSurferColorLUT.txt --i Vol_906_Reg_Bold.nii --sum > Vol_906_aparc_aseg.stats > > Thanks! > > -S > > > On Sun, May 26, 2013 at 11:11 AM, Salil Soman wrote: > >> Dear Doug, >> >> Thank you for your email. Following up on our previous discussions: >> >> 1) *bbregister fail *- this was happening because of error from >> fslregister. The variable fsvol was translating to "ERROR". In fslregister >> th value for fsvol is set to brainmask, along with numerous other >> parameters being initialized. >> By adding the line "set fsvol = brain mask" (without quotes) at the >> beginning of the section "#Convert reference to analyze" the CentOS 6 >> version I am running on ubuntu 12.04 (with SGE), now works. >> >> 2) when you suggested I run bbregister on the lowb.nii file, was it >> because I had suggested I wanted to register to a 2D ADC map? If I want to >> instead use a 3D volume (e.g. a 3D ASL), would I use the actual volume I >> want to get value from instead of lowb.nii? I ended up running >> >> 3) for the mri_vol2vol step - I had to change targ to fstarg, and I left >> out the interp flag so it would do its default trilinear: mri_vol2vol >> --mov Vol_906.nii --fstarg T1.mgz --o Vol_906_Reg_Bold.nii --no-save-reg >> --reg register_bold.dat --inv >> >> 4) I would like to get the segmentations from aparc+aseg.mgz as the areas >> where I get the values summed. So I entered mri_segstats --seg >> mri/aparc+aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i >> Vol_906_Reg_Bold.nii --sum Vol_aparc_aseg.stats >> >> but then I received this error: >> >> ERROR: dimension mismatch between input volume and seg >> input 224 224 170 >> seg 256 256 256 >> * >> * >> *So, in summary, while I've fixed bbregister to work on my system, I am >> still having trouble normalizing my 3D non T1 volume data into the FS space >> to be able to use the labels from aparc+aseg.mgz to get statistics for each >> anatomic area.* >> >> Any ideas on how to proceed? >> >> Thanks, >> >> Sal >> >> >> On Sat, May 25, 2013 at 11:51 AM, Douglas Greve < >> gr...@nmr.mgh.harvard.edu> wrote: >> >>> >>> On 5/25/13 1:39 PM, Salil Soman wrote: >>> >>> Thank you Doug. >>> >>> Just so I am clear - is the anatomical the nifti T1.mgz or is it a >>> different file. From your email I gather should do the following: >>> >>> *1) Use bbregister to register the lowb image to the anatomical. This >>> creates a registration matrix.* >>> >>> bbregister -s SUBJECTNAME --mov lowb.nii --initfsl --reg register.dat >>> >>> That is right, but add --t2 (since it is t2 weighted). >>> >>> >>> *2) Use mri_vol2vol and the registration to map the ADC map to the >>> anatomical* >>> >>> mri_vol2vol --mov lowb.nii --targ $vol --inv --interp nearest --o $vol2diff >>> --reg $outdir/register.dat --no-save-reg >>> >>> Use the ADC as the moveable (not lowb, but use the lowb for >>> bbregister). The target volume should be the T1.mgz (or any conformed >>> volume). The output will be the adc in the anatomical space (not sure why >>> you call it vol2diff). >>> >>>*3) use mri_segstats to extract the values* >>> >>> *mri_segstats* --seg $SUBJECTS_DIR/SUBJECTNAME/mri/wmparc.mgz --ctab >>> $FREESURFER_HOME/FreeSurferColorLUT.txt --i lowb.nii --sum fa.stats >>> >>> The input would be the adc volume mapped the anatomical space. I >>> would use WMParcStatsLUT.txt or else you'll get a billion different areas >>> not represented in wmparc. You may also want to add "--seg-erode 1" to >>> erode the segmentations by a voxel. This helps to prevent partial voluming. >>> >>> doug >>> >>> >>> >>> Where lowb.nii is the other MRI tissue sequence I am analyzing (e.g. >>> ADC), $vol2diff is the o
[Freesurfer] no hippocampal stats despite running FS 5.3 with -hippo-subfields
Dear Freesurfer Experts, I have been running freesurfer 5.3 without any reported errors using the following command: recon-all -i SPGR/*.gz -s SUBJECTIDENTIFIER -nuintensitycor-3T -nocanorm -openmp 50 -hippo-subfields -all However, when I look for any of the hippocampal subfield stats (as described on http://ftp.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation), I do not find any of them. Any suggestions on what I am doing incorrectly? Best wishes, Salil Soman, MD, MS ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] no hippocampal stats despite running FS 5.3 with -hippo-subfields
I can add that running the -hippo-subfields flag separately did work: recon-all -s SUBJECTIDENTIFIER -hippo-subfields Is there a reason the order of processing should matter? Is there a way I can change my recon-all call (below) so that hippo-subfields will get processed (so I do not have to make a separate call)? recon-all -i SPGR/*.gz -s SUBJECTIDENTIFIER -nuintensitycor-3T -nocanorm -openmp 50 -hippo-subfields -all Thank you, Sal On Sun, May 26, 2013 at 2:33 PM, Salil Soman wrote: > Dear Freesurfer Experts, > > I have been running freesurfer 5.3 without any reported errors using the > following command: > > recon-all -i SPGR/*.gz -s SUBJECTIDENTIFIER -nuintensitycor-3T -nocanorm > -openmp 50 -hippo-subfields -all > > However, when I look for any of the hippocampal subfield stats (as > described on > http://ftp.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation), I > do not find any of them. > > Any suggestions on what I am doing incorrectly? > > Best wishes, > > Salil Soman, MD, MS > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences
Thank you Doug, I think I initially misinderstood a number of things about this process. I have a 3D GRE volume (I guessed its contrast is closest to BOLD, bbregister set to T1 or T2 seemed to work more poorly). It is not a 2D. I would like to transform the 3D GRE volume into freesurfer space, so mri_segstats can use the segmentations from aparc+aseg.mgz to give back mean intensity values for each anatomic area. I could not find a file called lowb.nii, and so was not sure how to proceed. 1) do I need to use the file you mentioned (lowb.nii) - and if so, where would I find the file? 2) so running "mri_vol2vol --mov Vol_906.nii --fstarg T1.mgz --o Vol_906_Reg_Bold.nii --no-save-reg --reg register_bold.dat" (note inv left off) should map the 3D volume (Vol_906.nii) into the T1 space? Thank you for all of your help. Best wishes, Sal On Mon, May 27, 2013 at 7:23 PM, Douglas Greve wrote: > > On 5/26/13 2:11 PM, Salil Soman wrote: > >Dear Doug, > > Thank you for your email. Following up on our previous discussions: > > 1) *bbregister fail *- this was happening because of error from > fslregister. The variable fsvol was translating to "ERROR". In fslregister > th value for fsvol is set to brainmask, along with numerous other > parameters being initialized. > By adding the line "set fsvol = brain mask" (without quotes) at the > beginning of the section "#Convert reference to analyze" the CentOS 6 > version I am running on ubuntu 12.04 (with SGE), now works. > > see previous msg. > > > 2) when you suggested I run bbregister on the lowb.nii file, was it > because I had suggested I wanted to register to a 2D ADC map? If I want to > instead use a 3D volume (e.g. a 3D ASL), would I use the actual volume I > want to get value from instead of lowb.nii? I ended up running > > Oh, I did not realize it was a 2D map. Why do you have a 2D map instead of > 3D? That might be hard to get registered. You could have used the ADC or > FA. In general, you don't want to use the contrast that you will later be > testing as it creates a little bit of circularity. It is not much though, > and it should be fine. > > > 3) for the mri_vol2vol step - I had to change targ to fstarg, and I left > out the interp flag so it would do its default trilinear: mri_vol2vol > --mov Vol_906.nii --fstarg T1.mgz --o Vol_906_Reg_Bold.nii --no-save-reg > --reg register_bold.dat --inv > > that maps T1 into the bold space. Is that what you want? If you want to > map the bold into the anatomical space, then leave off -inv. This will also > solve your problem below > doug > > > 4) I would like to get the segmentations from aparc+aseg.mgz as the areas > where I get the values summed. So I entered mri_segstats --seg > mri/aparc+aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i > Vol_906_Reg_Bold.nii --sum Vol_aparc_aseg.stats > > > > but then I received this error: > > ERROR: dimension mismatch between input volume and seg > input 224 224 170 > seg 256 256 256 > * > * > *So, in summary, while I've fixed bbregister to work on my system, I am > still having trouble normalizing my 3D non T1 volume data into the FS space > to be able to use the labels from aparc+aseg.mgz to get statistics for each > anatomic area.* > > Any ideas on how to proceed? > > Thanks, > > Sal > > > On Sat, May 25, 2013 at 11:51 AM, Douglas Greve > wrote: > >> >> On 5/25/13 1:39 PM, Salil Soman wrote: >> >> Thank you Doug. >> >> Just so I am clear - is the anatomical the nifti T1.mgz or is it a >> different file. From your email I gather should do the following: >> >> *1) Use bbregister to register the lowb image to the anatomical. This >> creates a registration matrix.* >> >> bbregister -s SUBJECTNAME --mov lowb.nii --initfsl --reg register.dat >> >> That is right, but add --t2 (since it is t2 weighted). >> >> >> *2) Use mri_vol2vol and the registration to map the ADC map to the >> anatomical* >> >> mri_vol2vol --mov lowb.nii --targ $vol --inv --interp nearest --o $vol2diff >> --reg $outdir/register.dat --no-save-reg >> >>Use the ADC as the moveable (not lowb, but use the lowb for >> bbregister). The target volume should be the T1.mgz (or any conformed >> volume). The output will be the adc in the anatomical space (not sure why >> you call it vol2diff). >> >> *3) use mri_segstats to extract the values* >> >> *mri_segstats* --seg $SUBJECTS_DIR/SUBJECTNAME/mri/wmparc.mgz --ctab >> $FREESURFER_HOME/FreeSurferColorLUT.txt --i lowb.nii --sum fa.stats >> >>The input would be the adc vol
[Freesurfer] possible to display data obtained through mri_segment as heatmap?
Dear Doug, Thank you for your recent advise with using freesurfer to extract mean values from non structural image data. Is there a way to generate an image (e.g. heat map) displaying those values in free view? Best wishes, Sal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] possible to display data obtained through mri_segment as heatmap?
I have been able to generate the table. I was asking about an actual image (that could be visualized in freeview or something else). Thank you. -S On Fri, May 31, 2013 at 12:25 PM, Douglas N Greve wrote: > Do you mean table data or data that you have on a map? > > On 05/31/2013 03:20 PM, Salil Soman wrote: > >> Dear Doug, >> >> Thank you for your recent advise with using freesurfer to extract mean >> values from non structural image data. Is there a way to generate an image >> (e.g. heat map) displaying those values in free view? >> >> Best wishes, >> >> Sal >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: > surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** > greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. > If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] possible to display data obtained through mri_segment as heatmap?
Dear Doug, Thank you for your response. I am not sure I understand what I would be overlaying. I would like to display the T1 volume for the subject, but for each voxel color value, I would like that to reflect the mean intensity value that I calculated using mri_segstats. I do not see a way to do this in freeview. Any pointers to further details would be greatly appreciated. Best wishes, Sal On Fri, May 31, 2013 at 12:46 PM, Douglas N Greve wrote: > you can just specify an overlay on the freeview command line > > > On 05/31/2013 03:26 PM, Salil Soman wrote: > >> I have been able to generate the table. I was asking about an actual >> image (that could be visualized in freeview or something else). >> >> Thank you. >> >> -S >> >> >> On Fri, May 31, 2013 at 12:25 PM, Douglas N Greve < >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu>> >> wrote: >> >> Do you mean table data or data that you have on a map? >> >> On 05/31/2013 03:20 PM, Salil Soman wrote: >> >> Dear Doug, >> >> Thank you for your recent advise with using freesurfer to >> extract mean values from non structural image data. Is there a >> way to generate an image (e.g. heat map) displaying those >> values in free view? >> >> Best wishes, >> >> Sal >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu >> > >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: >> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> FileDrop: >> https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> >> >> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> >> Outgoing: >> >> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/**greve/<ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> >> >> The information in this e-mail is intended only for the person to >> whom it is >> addressed. If you believe this e-mail was sent to you in error and >> the e-mail >> contains patient information, please contact the Partners >> Compliance HelpLine at >> >> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. >> If the e-mail was sent to >> you in error >> but does not contain patient information, please contact the >> sender and properly >> dispose of the e-mail. >> >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: > surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** > greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] possible to display data obtained through mri_segment as heatmap?
Thank you Doug. Any pointers you can provide on how to try out this process in Matlab would be great. Best wishes, Sal On Mon, Jun 3, 2013 at 11:19 AM, Douglas N Greve wrote: > we don't have a way to do this. With a little programming you could do > this in matlab. let me know if you need pointers > doug > > > On 06/01/2013 04:43 PM, Salil Soman wrote: > >> Dear Doug, >> >> Thank you for your response. I am not sure I understand what I would be >> overlaying. >> >> I would like to display the T1 volume for the subject, but for each voxel >> color value, I would like that to reflect the mean intensity value that I >> calculated using mri_segstats. I do not see a way to do this in freeview. >> Any pointers to further details would be greatly appreciated. >> >> Best wishes, >> >> Sal >> >> >> On Fri, May 31, 2013 at 12:46 PM, Douglas N Greve < >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu>> >> wrote: >> >> you can just specify an overlay on the freeview command line >> >> >> On 05/31/2013 03:26 PM, Salil Soman wrote: >> >> I have been able to generate the table. I was asking about an >> actual image (that could be visualized in freeview or >> something else). >> >> Thank you. >> >> -S >> >> >> On Fri, May 31, 2013 at 12:25 PM, Douglas N Greve >> > <mailto:gr...@nmr.mgh.harvard.**edu >> > >> <mailto:gr...@nmr.mgh.harvard.**edu >> >> <mailto:gr...@nmr.mgh.harvard.**edu >>> >> wrote: >> >> Do you mean table data or data that you have on a map? >> >> On 05/31/2013 03:20 PM, Salil Soman wrote: >> >> Dear Doug, >> >> Thank you for your recent advise with using freesurfer to >> extract mean values from non structural image data. Is >> there a >> way to generate an image (e.g. heat map) displaying those >> values in free view? >> >> Best wishes, >> >> Sal >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.**edu >> > >> <mailto:gr...@nmr.mgh.harvard.**edu >> >> <mailto:gr...@nmr.mgh.harvard.**edu >> >> Phone Number: 617-724-2358 >> > >> Fax: 617-726-7422 > >> > >> >> Bugs: >> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> >> <http://surfer.nmr.mgh.**harvard.edu/fswiki/**BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> > >> FileDrop: >> https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> >> >> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.**html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> > >> <http://www.nmr.mgh.harvard.**edu/facility/filedrop/index.** >> html <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html>> >> >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** >> greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> >> >> The information in this e-mail is intended only for the >> person to >> whom it is >> addressed. If you believe this e-mail was sent to you in >> error and >> the e-mail >> contains patient information, please contact the Partners >> Compliance HelpLine at >> >> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. >> If the e-mail was sent to >> you in error >> but does not contain patient information, please contact the >> sender and properly >> disp
[Freesurfer] Possible to generate connectivity map using FS and Tracula
Dear Doug, Is there a way to use the Freesurfer and Tracula output to compute connectivity maps? Thanks! Sal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] CUDA Error when runnign freesurfer
Hi, I am running freesurfer 5.3 on an ubuntu 13.04 with a nvidia card and the the CUDA drivers installed. I am getting the following error when I try using the use-cuda command: Testing for CUDA device: nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2012 NVIDIA Corporation Built on Fri_Sep_21_17:28:58_PDT_2012 Cuda compilation tools, release 5.0, V0.2.1221 Acquiring CUDA device Using default device ERROR: Unable to acquire a CUDA device! Linux Baldrick 3.5.0-27-generic #46-Ubuntu SMP Mon Mar 25 19:58:17 UTC 2013 x86_64 x86_64 x86_64 GNU/Linux I am running the following freesurfer command: recon-all -i 242.nii.gz -s 242_FS -nuintensitycor-3T -nocanorm -openmp 8 -use-cuda -hippo-subfields -all Any suggestions on how I can fix this problem? Best wishes, Sal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] NU_evaluate crash while running Longitudinal Analysis with FS 5.3
Hi, I have been trying to run the FS longitudinal analysis on a subject with 3 time points. I ran each time point thourgh FS, made the template, but when I run the last step I do not get mri/norm files and the output files state nu_evaluate: crashed while running mincmath (termination status = 768), see attached log. Any suggestions on what I am doing incorrectly? Best wishes, Sal Salil Soman, MD, MS RZ_1484_LONG_POST.o893489 Description: Binary data ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] NU_evaluate crash while running Longitudinal Analysis with FS 5.3
Thank you Martin. Turns out that our cluster had crashed and killed the task due to hard drive space limitations. Its all fixed now and have been able to go through the tutorial at http://ftp.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial for a single subject with 3 time points. One question that I have is what is the color key for the 3D images viewed in freeview or tksurf? My subject has some yellow, red, blue, gray areas, with the majority of the brain being light blue. I just wanted to make sure I understood exactly what the data is actually depicting. Best wishes, Sal On Thu, Jul 4, 2013 at 8:16 AM, Martin Reuter wrote: > Hi Sal, > > not sure why the nu correction is crashing for you. > > can you check how the > FS/RZ_1484_POST_FS.long.RZ_1484_Base/mri/orig.mgz > and rawavg.mgz look? > Also make sure the talariach.xfm is correct in the template (base). > > Next time please send the recon-all.log file (from the subject's scripts > directory). It gives us more information than just the screen output. > > Best, Martin > > On Jul 4, 2013, at 1:17 AM, Salil Soman wrote: > > Hi, > > I have been trying to run the FS longitudinal analysis on a subject with 3 > time points. I ran each time point thourgh FS, made the template, but when > I run the last step I do not get mri/norm files and the output files state > nu_evaluate: crashed while running mincmath (termination status = 768), see > attached log. Any suggestions on what I am doing incorrectly? > > Best wishes, > > Sal > > Salil Soman, MD, MS > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > - > Dr. Martin Reuter > Assistant in Neuroscience - Massachusetts General Hospital > Instructor in Neurology - Harvard Medical School > MGH / HMS / MIT > > A.A.Martinos Center for Biomedical Imaging > 149 Thirteenth Street, Suite 2301 > Charlestown, MA 02129 > > Phone: +1-617-724-5652 > Email: >mreu...@nmr.mgh.harvard.edu >reu...@mit.edu > Web : http://reuter.mit.edu > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] color scale for longitudinal analysis using freeview
Dear experts, Could someone point me to the color key for the output of the longitudinal analysis as viewed in freebies (as generated by the freesurfer longitudinal analysis tutorial)? Thank you, Sal Salil Soman, MD, MS ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] average/RB_all_2008-03-26.gca not found error
Hi, *Am running this command:* $FREESURFER_HOME/bin/recon-all -i 3DSPGR.nii.gz -s WCA_248_T1Q_FS -nuintensitycor-3T -nocanorm -openmp 50 -hippo-subfields -use-cuda -all *And am get this out put / error:* Testing for CUDA device: nvcc: NVIDIA (R) Cuda compiler driver Copyright (c) 2005-2012 NVIDIA Corporation Built on Fri_Sep_21_17:28:58_PDT_2012 Cuda compilation tools, release 5.0, V0.2.1221 Driver : 5.50 Runtime : 5.0 Acquiring CUDA device Using default device CUDA device: GeForce GTX 660 === NUMBER OF OPENMP THREADS = 50 === stable5 NVIDIA driver version info: NVRM version: NVIDIA UNIX x86_64 Kernel Module 319.32 Wed Jun 19 15:51:20 PDT 2013 ERROR: cannot find /usr/local/freesurfer/average/RB_all_2008-03-26.gca Any suggestions what I am doing incorrectly? Thank you, Sal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] average/RB_all_2008-03-26.gca not found error
Thank you for your email. Yes that v is what freesurfer home is set to. Somehow that GCA file (SMS numerous others) were missing from the averages folder. I manually chopped them from a different 5.3 install, but am not sure v why they are missing (I am the only person using this machine and did not delete anything from the averages folder). Now that I copied the files over the command I listed runs but crashes with the error mpr2mni305 failed. I get this error on a dataset I have already processed using freesurfer 5.3 centos 6 version without the use-cuda option. Any suggestions would be greatly appreciated. Best wishes, Sal Hi Salil what is FREESURFER_HOME set to? Is it /usr/local/freesurfer? Does /usr/local/freesurfer/average/**RB_all_2008-03-26.gca exist? cheers Bruce On Mon, 8 Jul 2013, Salil Soman wrote: Hi, > Am running this command: > > $FREESURFER_HOME/bin/recon-all -i 3DSPGR.nii.gz -s WCA_248_T1Q_FS > -nuintensitycor-3T -nocanorm -openmp 50 -hippo-subfields > -use-cuda -all > > And am get this out put / error: > > Testing for CUDA device: > nvcc: NVIDIA (R) Cuda compiler driver > Copyright (c) 2005-2012 NVIDIA Corporation > Built on Fri_Sep_21_17:28:58_PDT_2012 > Cuda compilation tools, release 5.0, V0.2.1221 > > Driver : 5.50 > Runtime : 5.0 > > Acquiring CUDA device > Using default device > CUDA device: GeForce GTX 660 > > > === NUMBER OF OPENMP THREADS = 50 === > stable5 > > NVIDIA driver version info: > NVRM version: NVIDIA UNIX x86_64 Kernel Module 319.32 Wed Jun 19 > 15:51:20 PDT 2013 > > ERROR: cannot find /usr/local/freesurfer/average/**RB_all_2008-03-26.gca > > Any suggestions what I am doing incorrectly? > > Thank you, > > Sal > > > The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] possible to use multiple B value DTI in Tracula?
Hi, I was wondering - is it possible to use DTI data of multiple B values in Tracula (acquired during the same session and same TE)? Best wishes, Sal Salil Soman, MD, MS ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] possible to use multiple B value DTI in Tracula?
Thank you. I can concatenate the 3 acquisitions (I have 1 b2500, and 2 b1000) into a single nifti file, and then arrange the bval and bvec files to match. I will give it a try. Thank you for all your help. Best wishes, Sal On Mon, Jul 22, 2013 at 11:11 AM, Anastasia Yendiki < ayend...@nmr.mgh.harvard.edu> wrote: > > Hi Sal - Are these different scans that you want to merge? If they're all > in one file, then you just define the b-value for each frame as usual in > the bvalfile. There's no rule that all the b-values have to be the same. > > Hope this helps, > a.y > > > On Sun, 21 Jul 2013, Salil Soman wrote: > > Hi, >> I was wondering - is it possible to use DTI data of multiple B values in >> Tracula (acquired during the same session and same TE)? >> >> Best wishes, >> >> Sal >> >> Salil Soman, MD, MS >> >> >> > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. > If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Best way to generate Complete Stats Table
Hi, I have a large dataset for which I run freesurfer and confirmed that the apar+aseg.mgz file is satisfactory. Can someone please recommend the best way to aggregate all of the volumes/other values generated by freesurfer into a single table for this dataset? (e.g. subjects as Rows and values by columns). Best wishes, Sla ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Best way to generate Complete Stats Table
Thank you Doug! -S On Sun, Aug 4, 2013 at 10:09 AM, Douglas Greve wrote: > use asegstats2table and aparcstats2table. This will give you 3 tables > which you could then merge into 1. > doug > > > > On 8/4/13 12:22 PM, Salil Soman wrote: > >> Hi, >> >> I have a large dataset for which I run freesurfer and confirmed that the >> apar+aseg.mgz file is satisfactory. Can someone please recommend the best >> way to aggregate all of the volumes/other values generated by freesurfer >> into a single table for this dataset? (e.g. subjects as Rows and values by >> columns). >> >> Best wishes, >> >> Sla >> > > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. > If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Best way to generate Complete Stats Table
Dear Doug and Bruce, Thank you for your emails. I have also run the -hippo-subfields option on my freesurfer processing. How do I extract those values as tables as well? Best wishes, Sal On Sun, Aug 4, 2013 at 11:10 AM, Bruce Fischl wrote: > try asegstats2table > > cheers > Bruce > > On Sun, 4 Aug 2013, Salil Soman wrote: > > Hi, >> I have a large dataset for which I run freesurfer and confirmed that the >> apar+aseg.mgz file is satisfactory. Can someone please recommend the best >> way to aggregate all of the volumes/other values generated by freesurfer >> into a single table for this dataset? (e.g. subjects as Rows and values by >> columns). >> >> Best wishes, >> >> Sla >> >> >> > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. > If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] tksurfer and mountain lion problem / question
Hi, I can run freeview using my current install on Mountain Lion, however when I run tkmedit or tksurfer I get the following error: GLUT: Fatal Error in tksurfer.bin: could not open display: :0.0 my /etc/profile has the setting export DISPLAY=:0.0 for a different program. Is there settings I should add / change to allow tkmedit or tksurfer to run? Thanks! Sal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Best way to generate Complete Stats Table
Thank you! -Sal On Mon, Aug 5, 2013 at 2:22 PM, Douglas Greve wrote: > > Good question:). It does not look like we are currently creating a stats > file for the subfields, which means you will have to do it yourself. You > can do it with something like > > cd $SUBJECTS_DIR/subject > mri_segstats --seg mri/hippsubfieldseg.mgz --sum stats/hipposub.stats --pv > mri/norm.mgz --excludeid 0 --brain-vol-from-seg --brainmask > mri/brainmask.mgz --in mri/norm.mgz --in-intensity-name norm > --in-intensity-units MR --subject subject --surf-wm-vol --etiv --ctab > $FREESURFERHOME/FreeSurferColorLUT.txt > > You can then run asegstats2table specifying hipposub.stats as the stats > file > > doug > > > > > > On 8/5/13 3:39 PM, Salil Soman wrote: > > Dear Doug and Bruce, > > Thank you for your emails. I have also run the -hippo-subfields option > on my freesurfer processing. How do I extract those values as tables as > well? > > Best wishes, > > Sal > > > On Sun, Aug 4, 2013 at 11:10 AM, Bruce Fischl > wrote: > >> try asegstats2table >> >> cheers >> Bruce >> >> On Sun, 4 Aug 2013, Salil Soman wrote: >> >> Hi, >>> I have a large dataset for which I run freesurfer and confirmed that the >>> apar+aseg.mgz file is satisfactory. Can someone please recommend the best >>> way to aggregate all of the volumes/other values generated by freesurfer >>> into a single table for this dataset? (e.g. subjects as Rows and values >>> by >>> columns). >>> >>> Best wishes, >>> >>> Sla >>> >>> >>> >> >> The information in this e-mail is intended only for the person to whom >> it is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> > > > -- > Salil Soman, MD, MS > Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory > Fellow - Palo Alto War Related Illness and Injury Study Center > WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care > System > > > -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Best way to generate Complete Stats Table
On Mon, Aug 5, 2013 at 2:22 PM, Douglas Greve wrote: > mri/hippsubfieldseg.mgz Thank you Doug. Just to clarify the code you suggested earlier, should "mri/hippsubfieldseg.mgz" be replaced with each of the specific hipposubfields: posterior_Left-Cerebral-Cortex.mgz posterior_Left-Cerebral-White-Matter.mgz posterior_Left-Hippocampus.mgz posterior_Right-Cerebral-Cortex.mgz posterior_Right-Cerebral-White-Matter.mgz posterior_Right-Hippocampus.mgz posterior_left_CA1.mgz posterior_left_CA2_3.mgz posterior_left_CA4_DG.mgz posterior_left_fimbria.mgz posterior_left_hippocampal_fissure.mgz posterior_left_presubiculum.mgz posterior_left_subiculum.mgz posterior_right_CA1.mgz posterior_right_CA2_3.mgz posterior_right_CA4_DG.mgz posterior_right_fimbria.mgz posterior_right_hippocampal_fissure.mgz posterior_right_presubiculum.mgz posterior_right_subiculum.mgz If not, I do not see a file called mri/hippsubfieldseg.mgz for my output, and any advice on where I could find it would be great. Best wishes, Sal -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Best way to generate Complete Stats Table
Hi Doug, I realize now that I was unclear of the function of kvlQuantifyHippocampalSubfieldSegmentations.sh It creates a summary file of volumes for the left and right subfields as volumeStats_X.txt (where x is left or right). It writes the files into the mri subdirectory. Is there a scripted way to combine these stat files into a table format for a group? Thank you for all your help. Sal On Tue, Aug 6, 2013 at 12:17 PM, Douglas N Greve wrote: > oh, sorry, you are right. I had thought that they generated a single file > with the segmentations. In this case, you will need to threshold at some > value of the posterior probability. Alternatively, you could generate a > segmentation file by selecting the seg at a voxel that has the highest post > prob using mri_concat with the --max-index-prune option. You'd then create > your own LUT and run mri_segstats using the seg volume and the LUT > doug > > > On 08/06/2013 03:09 PM, Salil Soman wrote: > > >> On Mon, Aug 5, 2013 at 2:22 PM, Douglas Greve >> > gr...@nmr.mgh.harvard.**edu >> wrote: >> >> mri/hippsubfieldseg.mgz >> >> >> Thank you Doug. Just to clarify the code you suggested earlier, should >> "mri/hippsubfieldseg.mgz" be replaced with each of the specific >> hipposubfields: >> >> posterior_Left-Cerebral-**Cortex.mgz >> posterior_Left-Cerebral-White-**Matter.mgz >> posterior_Left-Hippocampus.mgz >> posterior_Right-Cerebral-**Cortex.mgz >> posterior_Right-Cerebral-**White-Matter.mgz >> posterior_Right-Hippocampus.**mgz >> posterior_left_CA1.mgz >> posterior_left_CA2_3.mgz >> posterior_left_CA4_DG.mgz >> posterior_left_fimbria.mgz >> posterior_left_hippocampal_**fissure.mgz >> posterior_left_presubiculum.**mgz >> posterior_left_subiculum.mgz >> posterior_right_CA1.mgz >> posterior_right_CA2_3.mgz >> posterior_right_CA4_DG.mgz >> posterior_right_fimbria.mgz >> posterior_right_hippocampal_**fissure.mgz >> posterior_right_presubiculum.**mgz >> posterior_right_subiculum.mgz >> >> >> If not, I do not see a file called mri/hippsubfieldseg.mgz for my output, >> and any advice on where I could find it would be great. >> >> Best wishes, >> >> Sal >> >> -- >> Salil Soman, MD, MS >> Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory >> Fellow - Palo Alto War Related Illness and Injury Study Center >> WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care >> System >> > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > gr...@nmr.mgh.harvard.edu > Phone Number: 617-724-2358 > Fax: 617-726-7422 > > Bugs: > surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> > FileDrop: > https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> > www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> > Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** > greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> > > > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. > If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Best way to generate Complete Stats Table
I can add that after running "kvlQuantifyHippocampalSubfield Segmentations.sh" I cannot find the nonPartialVolumeStatsLeft.txt and nonPartialVolumeStatsRigt.txt files mentioned on the tutorial page: http://ftp.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation I only have the volumeStats_left.txt and volumeStats_right.txt files in the mri subdirectory. Again, any pointers on how to generate group stats into a table would be a great help. Best wishes, Sal On Tue, Aug 6, 2013 at 12:33 PM, Salil Soman wrote: > Hi Doug, > > I realize now that I was unclear of the function > of kvlQuantifyHippocampalSubfieldSegmentations.sh > > It creates a summary file of volumes for the left and right subfields as > volumeStats_X.txt (where x is left or right). It writes the files into the > mri subdirectory. Is there a scripted way to combine these stat files into > a table format for a group? > > Thank you for all your help. > > Sal > > > On Tue, Aug 6, 2013 at 12:17 PM, Douglas N Greve < > gr...@nmr.mgh.harvard.edu> wrote: > >> oh, sorry, you are right. I had thought that they generated a single file >> with the segmentations. In this case, you will need to threshold at some >> value of the posterior probability. Alternatively, you could generate a >> segmentation file by selecting the seg at a voxel that has the highest post >> prob using mri_concat with the --max-index-prune option. You'd then create >> your own LUT and run mri_segstats using the seg volume and the LUT >> doug >> >> >> On 08/06/2013 03:09 PM, Salil Soman wrote: >> >> >>> On Mon, Aug 5, 2013 at 2:22 PM, Douglas Greve >>> >> gr...@nmr.mgh.harvard.**edu >> wrote: >>> >>> mri/hippsubfieldseg.mgz >>> >>> >>> Thank you Doug. Just to clarify the code you suggested earlier, should >>> "mri/hippsubfieldseg.mgz" be replaced with each of the specific >>> hipposubfields: >>> >>> posterior_Left-Cerebral-**Cortex.mgz >>> posterior_Left-Cerebral-White-**Matter.mgz >>> posterior_Left-Hippocampus.mgz >>> posterior_Right-Cerebral-**Cortex.mgz >>> posterior_Right-Cerebral-**White-Matter.mgz >>> posterior_Right-Hippocampus.**mgz >>> posterior_left_CA1.mgz >>> posterior_left_CA2_3.mgz >>> posterior_left_CA4_DG.mgz >>> posterior_left_fimbria.mgz >>> posterior_left_hippocampal_**fissure.mgz >>> posterior_left_presubiculum.**mgz >>> posterior_left_subiculum.mgz >>> posterior_right_CA1.mgz >>> posterior_right_CA2_3.mgz >>> posterior_right_CA4_DG.mgz >>> posterior_right_fimbria.mgz >>> posterior_right_hippocampal_**fissure.mgz >>> posterior_right_presubiculum.**mgz >>> posterior_right_subiculum.mgz >>> >>> >>> If not, I do not see a file called mri/hippsubfieldseg.mgz for my >>> output, and any advice on where I could find it would be great. >>> >>> Best wishes, >>> >>> Sal >>> >>> -- >>> Salil Soman, MD, MS >>> Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory >>> Fellow - Palo Alto War Related Illness and Injury Study Center >>> WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care >>> System >>> >> >> -- >> Douglas N. Greve, Ph.D. >> MGH-NMR Center >> gr...@nmr.mgh.harvard.edu >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: >> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> FileDrop: >> https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2> >> www.nmr.mgh.harvard.edu/**facility/filedrop/index.html<http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> Outgoing: ftp://surfer.nmr.mgh.harvard.**edu/transfer/outgoing/flat/** >> greve/ <ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/> >> >> >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. >> If the e-mail was sent to you in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> > >
Re: [Freesurfer] Best way to generate Complete Stats Table
Hi Doug, Turns out the kvlQuantifyHippocampalSubfieldSegmentations.sh was crashing before it got a chance to write the summary files. It crashed after trying to go into fsaverage/mri. I edited the file to specifically only go into my current study folders (they all have a common prefix), and then the script worked and generated the 2 summary files. Best wishes, Sal On Tue, Aug 6, 2013 at 12:40 PM, Salil Soman wrote: > I can add that after running "kvlQuantifyHippocampalSubfield > Segmentations.sh" I cannot find the nonPartialVolumeStatsLeft.txt > and nonPartialVolumeStatsRigt.txt files mentioned on the tutorial page: > > http://ftp.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation > > I only have the volumeStats_left.txt and volumeStats_right.txt files in > the mri subdirectory. > > Again, any pointers on how to generate group stats into a table would be a > great help. > > Best wishes, > > Sal > > > On Tue, Aug 6, 2013 at 12:33 PM, Salil Soman wrote: > >> Hi Doug, >> >> I realize now that I was unclear of the function >> of kvlQuantifyHippocampalSubfieldSegmentations.sh >> >> It creates a summary file of volumes for the left and right subfields as >> volumeStats_X.txt (where x is left or right). It writes the files into the >> mri subdirectory. Is there a scripted way to combine these stat files into >> a table format for a group? >> >> Thank you for all your help. >> >> Sal >> >> >> On Tue, Aug 6, 2013 at 12:17 PM, Douglas N Greve < >> gr...@nmr.mgh.harvard.edu> wrote: >> >>> oh, sorry, you are right. I had thought that they generated a single >>> file with the segmentations. In this case, you will need to threshold at >>> some value of the posterior probability. Alternatively, you could generate >>> a segmentation file by selecting the seg at a voxel that has the highest >>> post prob using mri_concat with the --max-index-prune option. You'd then >>> create your own LUT and run mri_segstats using the seg volume and the LUT >>> doug >>> >>> >>> On 08/06/2013 03:09 PM, Salil Soman wrote: >>> >>> >>>> On Mon, Aug 5, 2013 at 2:22 PM, Douglas Greve < >>>> gr...@nmr.mgh.harvard.edu >>>> <mailto:gr...@nmr.mgh.harvard.**edu>> >>>> wrote: >>>> >>>> mri/hippsubfieldseg.mgz >>>> >>>> >>>> Thank you Doug. Just to clarify the code you suggested earlier, should >>>> "mri/hippsubfieldseg.mgz" be replaced with each of the specific >>>> hipposubfields: >>>> >>>> posterior_Left-Cerebral-**Cortex.mgz >>>> posterior_Left-Cerebral-White-**Matter.mgz >>>> posterior_Left-Hippocampus.mgz >>>> posterior_Right-Cerebral-**Cortex.mgz >>>> posterior_Right-Cerebral-**White-Matter.mgz >>>> posterior_Right-Hippocampus.**mgz >>>> posterior_left_CA1.mgz >>>> posterior_left_CA2_3.mgz >>>> posterior_left_CA4_DG.mgz >>>> posterior_left_fimbria.mgz >>>> posterior_left_hippocampal_**fissure.mgz >>>> posterior_left_presubiculum.**mgz >>>> posterior_left_subiculum.mgz >>>> posterior_right_CA1.mgz >>>> posterior_right_CA2_3.mgz >>>> posterior_right_CA4_DG.mgz >>>> posterior_right_fimbria.mgz >>>> posterior_right_hippocampal_**fissure.mgz >>>> posterior_right_presubiculum.**mgz >>>> posterior_right_subiculum.mgz >>>> >>>> >>>> If not, I do not see a file called mri/hippsubfieldseg.mgz for my >>>> output, and any advice on where I could find it would be great. >>>> >>>> Best wishes, >>>> >>>> Sal >>>> >>>> -- >>>> Salil Soman, MD, MS >>>> Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory >>>> Fellow - Palo Alto War Related Illness and Injury Study Center >>>> WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care >>>> System >>>> >>> >>> -- >>> Douglas N. Greve, Ph.D. >>> MGH-NMR Center >>> gr...@nmr.mgh.harvard.edu >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: >>> surfer.nmr.mgh.harvard.edu/**fswiki/BugReporting<http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >>> FileDrop: >>> https://gate.nmr.mgh.harvard.**edu/filedrop2<https://gate.nmr.mgh.harvard.edu/filedrop2&g
[Freesurfer] preferred method for generating appropriate bvecs for tracula
Hi, I have dicoms that I turn to nifti using dcm2nii (with the default settings plus anonymization option turned on [-a y]). The bvec files it generates by default are 3 rows by n columns (where n is b0 number + directions). I am under the impression tracula requires this to be converted to a n row by 3 column file. 1) is this correct, 2) is there a preferred way to perform this transformation on linux systems? Thanks you, -Sal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] preferred method for generating appropriate bvecs for tracula
Thank you for the email.
I saw a warning to check for flipping L-R from the dcm2nii site:
http://www.mccauslandcenter.sc.edu/mricro/mricron/dcm2nii.html
Is the problem you mentioned vendor specific (I have all GE data). Is there
a different tool you would recommend for generating the bvec files? I would
prefer to run tracula right off the original dicom images but transferring
them to the cluster and anonymizing them would be prohibitively difficult.
I could not find the freesurfer archive message you referred to. Any
pointers would be greatly appreciated.
Best wishes,
Sal
On Wed, Aug 7, 2013 at 1:12 PM, Anastasia Yendiki <
ayend...@nmr.mgh.harvard.edu> wrote:
>
> set x = `cat bvecs | awk '{if (NR==1) print}'`
> set y = `cat bvecs | awk '{if (NR==2) print}'`
> set z = `cat bvecs | awk '{if (NR==3) print}'`
>
> @ k = 1
> while ( $k <= `head -1 bvecs|wc -w` )
> echo $x[$k] $y[$k] $z[$k]
> @ k = $k + 1
> end
>
> I'd make sure though dcm2nii doesn't L-R flip the gradient vectors, I
> think there was a thread recently that suggested it might.
>
>
> On Wed, 7 Aug 2013, Salil Soman wrote:
>
> Hi,
>> I have dicoms that I turn to nifti using dcm2nii (with the default
>> settings plus anonymization option turned on [-a
>> y]). The bvec files it generates by default are 3 rows by n columns
>> (where n is b0 number + directions). I am under
>> the impression tracula requires this to be converted to a n row by 3
>> column file. 1) is this correct, 2) is there a
>> preferred way to perform this transformation on linux systems?
>>
>> Thanks you,
>>
>> -Sal
>>
>>
>>
>
> The information in this e-mail is intended only for the person to whom it
> is
> addressed. If you believe this e-mail was sent to you in error and the
> e-mail
> contains patient information, please contact the Partners Compliance
> HelpLine at
> http://www.partners.org/**complianceline<http://www.partners.org/complianceline>.
> If the e-mail was sent to you in error
> but does not contain patient information, please contact the sender and
> properly
> dispose of the e-mail.
>
>
--
Salil Soman, MD, MS
Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory
Fellow - Palo Alto War Related Illness and Injury Study Center
WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System
___
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The information in this e-mail is intended only for the person to whom it is
addressed. If you believe this e-mail was sent to you in error and the e-mail
contains patient information, please contact the Partners Compliance HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you in error
but does not contain patient information, please contact the sender and properly
dispose of the e-mail.
Re: [Freesurfer] preferred method for generating appropriate bvecs for tracula
Thank you for your response. Is there a best way to review the eigenvectors (tkmedit, freeview, other program?). Thank you. -S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] hippocampal subfields question
Hi, I just wanted to confirm that label "hippocampus" in the hippocampal subfields segmentation is simply parts of the hippocampus that do not fall into one of the other major categories? Also, where can I find the units for the hippocampal subfields? I am seeing some discrepancy between the left and right hippocampal volumes generated by freesurfer and the summed areas generated by the hippocampal subfield analysis. Thank you, -Sal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] freeview problem
Hi, When I try to run freeview on my ubuntu 13 machine, running the nvidia 5.0 cuda drivers, I get the following errors: Xlib: extension "NV-GLX" missing on display "localhost:10.0". Xlib: extension "NV-GLX" missing on display "localhost:10.0". Xlib: extension "NV-GLX" missing on display "localhost:10.0". Xlib: extension "NV-GLX" missing on display "localhost:10.0". X Error: GLXBadContext 150 Extension:143 (Uknown extension) Minor opcode: 5 (Unknown request) Resource id: 0x8000c0 X Error: GLXBadContext 150 Extension:143 (Uknown extension) Minor opcode: 5 (Unknown request) Resource id: 0x8000c0 X Error: GLXBadContext 150 Extension:143 (Uknown extension) Minor opcode: 5 (Unknown request) Resource id: 0x8000c0 Any suggestions on how i can fix this problem? Thanks! Sal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] freeview problem
Thank you Zeke. I am trying to run freeview remotely and display locally on a machine (using Xming). The computer from which I am connecting can successfully run freeview from a different ubuntu 13 machine (one which does not have a cuda graphics card / cuda drivers). When I run glxgears (required me to install mesa-utils), for the NV-GLX missing on display localhost:10.0. A window did popup via xming, but it was black. While it was up the remote machien kept listing x frames in y seconds = z fps The machine did have cuda 5.0 working with the nvidia 319 linux driver, so freesurfer could be gpu accerlated. Any suggestions on how to fix this would be great. A similar problem I would like to run by you is regarding the local display on the other ubunut machine I mentioned above. I can connect to this other machien remotely and run freeview, however if I actually use the local monitor attached to the machine, the frreeview window comes up, but in place of imaging data or black, it shows a kind of tie-dye color pattern. The rest of the screen is normal ubuntu, but the freeview window has problems. This other machine has an nivida card that predates cuda (and so no cuda drivers are installed). Any suggestions on how to fix this problem would also be a great help. Best wishes, Sal On Fri, Aug 16, 2013 at 8:13 AM, Z K wrote: > Hello Sal, > > Are your trying to run freeview remotely and display locally machine? If > you type 'glxgears' at the command line does a window popup displaying > spinning gears? > > -Zeke > > > > On 08/16/2013 05:55 AM, Salil Soman wrote: > >> Hi, >> >> When I try to run freeview on my ubuntu 13 machine, running the nvidia >> 5.0 cuda drivers, I get the following errors: >> >> Xlib: extension "NV-GLX" missing on display "localhost:10.0". >> Xlib: extension "NV-GLX" missing on display "localhost:10.0". >> Xlib: extension "NV-GLX" missing on display "localhost:10.0". >> Xlib: extension "NV-GLX" missing on display "localhost:10.0". >> X Error: GLXBadContext 150 >>Extension:143 (Uknown extension) >>Minor opcode: 5 (Unknown request) >>Resource id: 0x8000c0 >> X Error: GLXBadContext 150 >>Extension:143 (Uknown extension) >>Minor opcode: 5 (Unknown request) >>Resource id: 0x8000c0 >> X Error: GLXBadContext 150 >>Extension:143 (Uknown extension) >>Minor opcode: 5 (Unknown request) >>Resource id: 0x8000c0 >> >> Any suggestions on how i can fix this problem? >> >> Thanks! >> >> Sal >> >> >> __**_ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.**edu/mailman/listinfo/**freesurfer<https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer> >> >> > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine at > http://www.partners.org/**complianceline<http://www.partners.org/complianceline>. > If the e-mail was sent to you in error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] gradient table question for Tracula
Hi Anastasia, A question I had about the gradient tables for Tracula - I recently came across this passage from Hui Zhang: "To correct for any errors that you identify, you need to first modify the gradient table, then repeat the tensor reconstruction. The modification of the gradient table typically involves flipping the signs of the x or y component of all gradient vectors. To determine the correct flipping of the signs in a systematic way, it is necessary to understand why this happens. The reason is that the gradient directions are always defined with respect to some right-handed frame of reference, while the frame of reference of the acquired image data is typically NOT right-handed. This mismatch is the cause of the problem. The sign flipping intends to fix this mismatch and the key is to identify the difference between the two frames of reference in question. In our experience, if the data is acquired on SIEMENS scanners, the signs of x gradient components need to be flipped; for GE scanners, it is usually the y components." (from http://dti-tk.sourceforge.net/pmwiki/pmwiki.php?n=Documentation.VisualizationTool ). Does this mean that the gradient tables i get from dcm2nii need to have the Y component flipped for my GE acquisitions or is this adjusted in the tracula processing? Thank you. -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Clarification regarding bvec processing in TRACULA
Hi, After much searching, it appears to be pretty uniform that the product DTI sequence performed on GE requires the y gradient to be flipped. For the datasets with which I am working diffusion toolkit, vistalab and exploredti all require the y gradient to be flipped. However, Tracula makes appropriate outputs when I give it the default gradient table without flipping Y. When I flip Y and run it through Tracula, the forceps major is inverted (noted by checking the overlay of dtifit_fa and dtifit_V1 using fslview and by using TVglyphView using DTI-TK. I suspect that somehow Tracula is flipping the Y sign for the gradient (while the other programs I mentioned do not) - can anyone confirm this? Thanks! -Sal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] unable to download updated mri_segstats
Hi, The link ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats.linux from the release notes for freesurfer 5.1 ( http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes) appears broken. I also checked the anonymous ftp site and found only the directories bbr-papers and growth-curves within the /transfer/outgoing/flat/greve directory. Could someone please direct me to the correct download link for the updated file? Also, is there an updated version of mri_segstats for mac? Thank you. Salil Soman, MD, MS ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Clarification regarding eTIV
Dear List Members, I am planning to use the eTIV for a group analysis using segmentation volumes and I need to confirm that the eTIV ( aka ICV) generated in freesurfer is NOT dependent on the skull strip? Specifically, I wanted to make sure one does not need to QC the skull strips to make sure all of the brain structures suggested in that figure on p728 of the buckner paper ( http://surfer.nmr.mgh.harvard.edu/fswiki/eTIV?action=AttachFile&do=view&target=buckner2004.pdf) need to be included? Thanks, -S ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Tracula on cluster problem
Dear Freesurfer Experts,
I am running freesurfer (centos4 64 bit v5.10) and a fsl 5.0.2.1 (compiled
from source code) on a cluster running ubuntu 12.04 and the debian version
of sun grid engine. I have successfully run freesurfer and trac-all -prep
using this configuration. However, when I try to run trac-all -bedp -c
dmrirc_file, the process I get the following progress and abrupt
termination within a hour or so:
ln -sf
/mnt/glusterfs/myaccount/output/TRACULA/CRP_FS/dlabel/diff/aparc+aseg_mask.bbr.nii.gz
/mnt/glusterfs/myaccount/output/TRACULA/$
ln -sf /mnt/glusterfs/myaccount/output/TRACULA/CRP_FS/dmri/dwi.nii.gz
/mnt/glusterfs/myaccount/output/TRACULA/CRP_FS/dmri/data.nii.gz
WARN: Running FSL's bedbost locally - this might take a while
WARN: It is recommended to run this step on a cluster
bedpostx_seychelles /mnt/glusterfs/myaccount/output/TRACULA/CRP_FS/dmri
subjectdir is /mnt/glusterfs/myaccount/output/TRACULA/CRP_FS/dmri
Making bedpostx directory structure
Queuing preprocessing stages
Queuing parallel processing stage
0 slices processed
1 slices processed
1 slices processed
1 slices processed
1 slices processed
1 slices processed
1 slices processed
1 slices processed
1 slices processed
Queuing post processing stage
/mnt/glusterfs/myaccount/freesurfer/bin/bedpostx_seychelles: line 376:
14275 Terminated ${subjdir}.bedpostX/monitor
Any suggestions on what I am doing incorrectly?
Thank you,
Salil Soman, MD, MS
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[Freesurfer] corRead() error with Tracula / FS 5.2
Dear Experts, I am setup fs 5.2 and have successfully run freesurfer processing on a SPGR dataset. However, when I attempt to run Tracula on that dataset, I keep getting a corRead(): can't open file /path/to/ducks/COR-.info (where to path to ducks is the patch to where my subjects are located), with additional subsequent errors about b0mag.nii.gz not existing. My data is comprised of two consecutive 30 drxn plus 5 b0 GE product acquisitions, combined into 1 dataset using mri_concat. The data is then sliced int 2.5mm isotropic data using mri_convert. . The bvec file is create by transposing and then concatenating 2 bvec files outputed by dcm2nii using a perl script (the bval file is made in a similar way using the bval files outputted by dcm2nii). As I am trying to run this on a cluster, it is easier for me to deal in nifti's instead of dicoms, and so I am providing the anonymized isotropic nii file (as created by dcm2nii) as the input along with the bvec and bval files. I have tried checking the bval and bvec files for extra spaces/lines (using vi), and have not found any (as I had seen mentioned in other posts). Any suggestions on what I may be doing incorrectly would be greatly appreciated. Best wishes, Salil Soman ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files
Hi, I have run a number of cases through the FS6 hippocampal longitudinal processing steps listed at https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalHippocampalSubfields and https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing It seems that all steps completed, but when it came time to collect the results, I find I have many more lh.hippoSfVolumes-T1.long.v10.txt (67) than rh.hippoSfVolumes-T1.long.v10.txt files (25). Any suggestions on what I may be doing incorrectly? Thanks! Salil Soman ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] freesurfer 6 hippocampal longitudinal processing workflow question, more LH than RH files
Thank you for your email. Just to follow up, the rh and lh hippocampal hippoSfVolumes-T1.v10.txt files are present, but for a large number of cases, only the lh hippoSfVolumes-T1.long.v10.txt files are present. I reran the exact same recon-all -long command for all the cases, and I reran them after your suggestion, but there is no change in the number of missing rh.hippoSfVolumes-T1.long.v10.txt files. The log file for the longitudinal processing for recon-all says the process completed with no errors. Is there anything else I should check? Thanks! On Fri, Apr 14, 2017 at 3:54 AM Alan Francis wrote: > Hi Salil: > > It could be that the HSF script may have `errored out' mid way through the > analysis. If you go through the recon processing steps which are one of the > output files, you will see exactly where the error occurred. Just reprocess > that brain and see if that happens again. > > Hope this helps, > > best, > > Alan > > > > On Thu, Apr 13, 2017 at 4:49 PM, Salil Soman wrote: > >> Hi, >> >> I have run a number of cases through the FS6 hippocampal longitudinal >> processing steps listed at >> https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalHippocampalSubfields >> and https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing >> >> It seems that all steps completed, but when it came time to collect the >> results, I find I have many more lh.hippoSfVolumes-T1.long.v10.txt (67) >> than rh.hippoSfVolumes-T1.long.v10.txt files (25). Any suggestions on what >> I may be doing incorrectly? >> >> Thanks! >> >> Salil Soman >> >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> The information in this e-mail is intended only for the person to whom it >> is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> > > > -- > |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| > > *Alan N. Francis PhD* > Regional Sales Manager/ Application specialist > Nordic Neurolab > Boston. > a...@nordicneurolab.com > > > *Previously:* > Instructor - Imaging Neuroscience > Brain Imaging Center > McLean Hospital > Harvard Medical School > 115 Mill Street, Belmont, MA 02478 > al...@bwh.harvard.edu > afran...@mclean.harvard.edu > > > |~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~|~| > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] possible to enable openmp with tracula cvsreg?
Hi, I noticed in the output for tracula -prep I am currently running using cvsreg it mentions openmp=1, I was wondering if there is a way to enable more than 1 core for openmp for tracula-prep? Thanks, -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] tracula cvs_reg taking greater than 24 hours
Hi, I am running tracula prep step using doregcvs=1, and the case has been processing for greater than 1.5 days now. To get it to run, I had to follow the instructions from here: https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg36133.html Any suggestions if I am doing something wrong, or if I can expect this step to end? Thanks, S The latest output lines (over several hundred total) are below: -- unfolding failed - restoring original position 0003: dt=4.25, rms=0.867 (0.000%), neg=0, invalid=1530 setting smoothness coefficient to 2.000 blurring input image with Gaussian with sigma=0.250... : dt=0.000, rms=0.867, neg=0, invalid=1530 orig dt = 0 in gcamFindOptimalTimeStep iter 0, gcam->neg = 21980 after 238 iterations, nbhd size=2, neg = 551 starting rms=0.830, neg=551, removing folds in lattice iter 1, dt=2.048000: new neg 27008, old_neg 551, delta -26457, rms=0.780 (6.086%) Numerical result out of range orig dt = 0 in gcamFindOptimalTimeStep iter 2, dt=0.002294: new neg 23842, old_neg 27008, delta 3166, rms=0.772 (1.003%) Numerical result out of range orig dt = 0 in gcamFindOptimalTimeStep iter 3, dt=0.000573: new neg 23004, old_neg 23842, delta 838, rms=0.766 (0.745%) Numerical result out of range -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] how to pass openmp option to mri_cvs_register through Tracula-prep?
Hi, I noticed that openmp is set to 1 in mri_cvs_register. However, I do not see a way to pass on this parameter to to mri_cvs_register through dmrirc for tracula - prep. Can anyone point me to how this can be done? Thanks! Sal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] longitudinal QDEC question
Hi, I have been following the steps for longitudinal processing from here ( https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel), and was hoping for some advice on how to setup the GLM. I have a set of data where I have 2 time points for all subjects, have run recon-all, qcache, the base and cross steps of processing. I also ran the long mri_slopes step, created my long.qdec table, then created the simplified table for qdec. I would like to perform a whole brain analysis where I identify any brain regions that changed (volume or cortical thickness) from time point 1 and time point 2. I am a little unclear on what the explanatory variable should be performing this analysis. Any suggestions on how best to structure the analysis would be greatly appreciated. Best wishes, Salil Soman, MD, MS ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] question about qdec Stats Data Import for Longitudinal Workflow
When following the longitudinal qdec tutorial ( https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel), does using the generate Stats Data Tables option extract data for the difference between time point1 and 2, or something else? Thank you. Salil Soman, MD, MS ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] longitudinal freesurfer error
Hi, I have followed the steps in the longitudinal qdec tutorial ( https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel), but when I try to analyze longitudinal features such as long.thickness-rate I get an error: Error in analyze: Couldn't open /SUBJECTS_DIR/SUBJECT_ID/surf/lh.long.thickness-rate.fwhm10.fsaverage.mgz or .mgh file Any suggestions on what I am doing incorrectly? Best wishes, Sal -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Freesurfer longitudinal GLM Design question
Hi, I have been following the tutorial from here: https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/LongitudinalTutorial and here: https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalTwoStageModel And I believe I am running into problems with my GLM design. I have a set of subjects with 2 time points each (all about 0.1 years apart). All I wish to do is see what areas are significantly changed in volume, after correcting for multiple comparisons (fdr or montecarlo). Could anyone suggest how I should setup the Design in QDEC?. I have included years and age in my cross.qdec.table.dat file (made from my long.qdec.table.dat file as described the tutorial, and have the measures of long.thickness-avg, long.thickness-rate, long.thickness-pc1 and long.thickness-spc avaialble (again from the tutorial). Any advice would be greatly appreciated. Sal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Any good cortical segmentation methods for brains with infarct or tumors?
Hi, Does anyone have recommendations for good automated cortical segmentation tools for brains with infarct (so some brain missing) or tumors? I am under the impression that FreeSurfer is not reliable in these cases. If I am incorrect, any pointers on how to use FreeSurfer in these cases would be very helpful. Thank you. Salil Thanks ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences
Dear Doug, Thank you again for this email. Do you think it is possible to use this method for ASL images as well? If so, how would you change the options? Best wishes, Salil Soman, MD, MS On Sat, May 25, 2013 at 11:51 AM, Douglas Greve wrote: > > On 5/25/13 1:39 PM, Salil Soman wrote: > > Thank you Doug. > > Just so I am clear - is the anatomical the nifti T1.mgz or is it a > different file. From your email I gather should do the following: > > *1) Use bbregister to register the lowb image to the anatomical. This > creates a registration matrix.* > > bbregister -s SUBJECTNAME --mov lowb.nii --initfsl --reg register.dat > > That is right, but add --t2 (since it is t2 weighted). > > > *2) Use mri_vol2vol and the registration to map the ADC map to the > anatomical* > > mri_vol2vol --mov lowb.nii --targ $vol --inv --interp nearest --o $vol2diff > --reg $outdir/register.dat --no-save-reg > > Use the ADC as the moveable (not lowb, but use the lowb for > bbregister). The target volume should be the T1.mgz (or any conformed > volume). The output will be the adc in the anatomical space (not sure why > you call it vol2diff). > > *3) use mri_segstats to extract the values* > > *mri_segstats* --seg $SUBJECTS_DIR/SUBJECTNAME/mri/wmparc.mgz --ctab > $FREESURFER_HOME/FreeSurferColorLUT.txt --i lowb.nii --sum fa.stats > > The input would be the adc volume mapped the anatomical space. I would > use WMParcStatsLUT.txt or else you'll get a billion different areas not > represented in wmparc. You may also want to add "--seg-erode 1" to erode > the segmentations by a voxel. This helps to prevent partial voluming. > > doug > > > Where lowb.nii is the other MRI tissue sequence I am analyzing (e.g. > ADC), $vol2diff is the output image of the registration, and fa.stats will > be my output stats table? > > I suspect there is part of the syntax for these tools I do not > understand. Also, what input would $vol be? > > Best wishes, > > Sal > > > On Sat, May 25, 2013 at 10:06 AM, Douglas Greve > wrote: > >> >> Hi Sal, yes you can. Use bbregister to register the lowb image to the >> anatomical. This creates a registration matrix. Use mri_vol2vol and the >> registration to map the ADC map to the anatomical, then use mri_segstats to >> extract the values >> doug >> >> ps. Please post questions to the FS list instead of us directly so that >> others can benefit and it gets archived. thanks! >> >> >> >> On 5/25/13 1:03 PM, Salil Soman wrote: >> >>> Dear Dr. Greve, >>> >>> Is it possible to register a nonstructural MR sequences (e.g. an ADC >>> map) with the aseg.mgz file (or aparc+aseg.mgz file, etc) and then, using >>> the segmentation from the aseg (or aparc+aseg) file to output a mean ADC >>> value for each anatomic area segmented? >>> >>> Thank you for your time and consideration. >>> >>> Best wishes, >>> >>> Sal >>> >>> Salil Soman, MD, MS >>> >> >> >> >> The information in this e-mail is intended only for the person to whom >> it is >> addressed. If you believe this e-mail was sent to you in error and the >> e-mail >> contains patient information, please contact the Partners Compliance >> HelpLine at >> http://www.partners.org/complianceline . If the e-mail was sent to you >> in error >> but does not contain patient information, please contact the sender and >> properly >> dispose of the e-mail. >> >> > > -- Salil Soman, MD, MS Postdoctoral Research Fellow - Stanford Radiological Sciences Laboratory Fellow - Palo Alto War Related Illness and Injury Study Center WOC Neuroradiology Attending - Veterans Affairs Palo Alto Health Care System ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences
Thank you Doug. I am having trouble with extracting statistics using this method. I am able to use bbregister to get a transformation that registers the PD image of the ASL to the T1. I then used this transformation matrix to register the CBF map for the ASL study into the T1.mgz space. Checking the images, the registration looked reasonable. However, when I try to extract the values from the registered image using the vois from aparc+aseg.mgz, and the FreeSurferColorLUT I get all 0 values. *The command I ran is:* mri_segstats --seg $SUBJECTS_DIR/SUBJECT_ID/mri/aparc+aseg.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i SUBJECT_ID_CBF_reg.nii.gz --sum SUBJECT_ID_ASL.stats --seg-erode 1 *where SUBJECT_ID_CBF_reg.nii.gz was generated by running:* mri_vol2vol --mov SUBJECT_ID_CBF.nii.gz --targ T1.mgz --interp nearest --o SUBJECT_ID_CBF_reg.nii.gz --reg SUBJECT_ID.dat --no-save-reg (and this was run with T1.mgz and SUBJECT_ID_CBF.nii.gz in the same folder). *for which SUBJECT_ID.dat was generated by running the code:* bbregister --s SUBJECT_ID --mov SUBJECT_ID_ASL_PD.nii.gz --reg SUBJECT_ID.dat --t1 --init-fsl Thank you for your consideration of this question. Best wishes, Salil Soman, MD, MS On Sun, Sep 14, 2014 at 3:32 PM, Douglas Greve wrote: > yep, you can use it for anything. > doug > > > On 9/14/14 12:52 PM, Salil Soman wrote: > > Dear Doug, > > Thank you again for this email. Do you think it is possible to use this > method for ASL images as well? If so, how would you change the options? > > Best wishes, > > Salil Soman, MD, MS > > On Sat, May 25, 2013 at 11:51 AM, Douglas Greve > wrote: > >> >> On 5/25/13 1:39 PM, Salil Soman wrote: >> >> Thank you Doug. >> >> Just so I am clear - is the anatomical the nifti T1.mgz or is it a >> different file. From your email I gather should do the following: >> >> *1) Use bbregister to register the lowb image to the anatomical. This >> creates a registration matrix.* >> >> bbregister -s SUBJECTNAME --mov lowb.nii --initfsl --reg register.dat >> >> That is right, but add --t2 (since it is t2 weighted). >> >> >> *2) Use mri_vol2vol and the registration to map the ADC map to the >> anatomical* >> >> mri_vol2vol --mov lowb.nii --targ $vol --inv --interp nearest --o $vol2diff >> --reg $outdir/register.dat --no-save-reg >> >>Use the ADC as the moveable (not lowb, but use the lowb for >> bbregister). The target volume should be the T1.mgz (or any conformed >> volume). The output will be the adc in the anatomical space (not sure why >> you call it vol2diff). >> >> *3) use mri_segstats to extract the values* >> >> *mri_segstats* --seg $SUBJECTS_DIR/SUBJECTNAME/mri/wmparc.mgz --ctab >> $FREESURFER_HOME/FreeSurferColorLUT.txt --i lowb.nii --sum fa.stats >> >>The input would be the adc volume mapped the anatomical space. I >> would use WMParcStatsLUT.txt or else you'll get a billion different areas >> not represented in wmparc. You may also want to add "--seg-erode 1" to >> erode the segmentations by a voxel. This helps to prevent partial voluming. >> >> doug >> >> >> Where lowb.nii is the other MRI tissue sequence I am analyzing (e.g. >> ADC), $vol2diff is the output image of the registration, and fa.stats will >> be my output stats table? >> >> I suspect there is part of the syntax for these tools I do not >> understand. Also, what input would $vol be? >> >> Best wishes, >> >> Sal >> >> >> On Sat, May 25, 2013 at 10:06 AM, Douglas Greve < >> gr...@nmr.mgh.harvard.edu> wrote: >> >>> >>> Hi Sal, yes you can. Use bbregister to register the lowb image to the >>> anatomical. This creates a registration matrix. Use mri_vol2vol and the >>> registration to map the ADC map to the anatomical, then use mri_segstats to >>> extract the values >>> doug >>> >>> ps. Please post questions to the FS list instead of us directly so that >>> others can benefit and it gets archived. thanks! >>> >>> >>> >>> On 5/25/13 1:03 PM, Salil Soman wrote: >>> >>>> Dear Dr. Greve, >>>> >>>> Is it possible to register a nonstructural MR sequences (e.g. an ADC >>>> map) with the aseg.mgz file (or aparc+aseg.mgz file, etc) and then, using >>>> the segmentation from the aseg (or aparc+aseg) file to output a mean ADC >>>> value for each anatomic area segmented? >>>> >>>> Thank you for your time and consideration. >>>> >>>>
Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences
Dear Doug, Thank you for your email. The registration overlap looks reasonable. Thank you for considering this question. Best wishes, Sal On Thu, Sep 18, 2014 at 12:14 PM, Douglas N Greve wrote: > > When you look at SUBJECT_ID_CBF_reg.nii.gz, does it look reasonable? Does > it overlay correctly on the T1.mgz? > doug > > On 09/14/2014 11:40 PM, Salil Soman wrote: > >> Thank you Doug. I am having trouble with extracting statistics using >> this method. >> >> I am able to use bbregister to get a transformation that registers the PD >> image of the ASL to the T1. I then used this transformation matrix to >> register the CBF map for the ASL study into the T1.mgz space. Checking the >> images, the registration looked reasonable. However, when I try to extract >> the values from the registered image using the vois from aparc+aseg.mgz, >> and the FreeSurferColorLUT I get all 0 values. >> >> *The command I ran is:* >> >> mri_segstats --seg $SUBJECTS_DIR/SUBJECT_ID/mri/aparc+aseg.mgz --ctab >> $FREESURFER_HOME/FreeSurferColorLUT.txt --i SUBJECT_ID_CBF_reg.nii.gz >> --sum SUBJECT_ID_ASL.stats --seg-erode 1 >> >> *where SUBJECT_ID_CBF_reg.nii.gz was generated by running:* >> >> mri_vol2vol --mov SUBJECT_ID_CBF.nii.gz --targ T1.mgz --interp nearest >> --o SUBJECT_ID_CBF_reg.nii.gz --reg SUBJECT_ID.dat --no-save-reg >> >> (and this was run with T1.mgz and SUBJECT_ID_CBF.nii.gz in the same >> folder). >> >> *for which SUBJECT_ID.dat was generated by running the code:* >> >> bbregister --s SUBJECT_ID --mov SUBJECT_ID_ASL_PD.nii.gz --reg >> SUBJECT_ID.dat --t1 --init-fsl >> >> Thank you for your consideration of this question. >> >> Best wishes, >> >> Salil Soman, MD, MS >> >> >> >> >> On Sun, Sep 14, 2014 at 3:32 PM, Douglas Greve > <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> >> yep, you can use it for anything. >> doug >> >> >> On 9/14/14 12:52 PM, Salil Soman wrote: >> >>> Dear Doug, >>> >>> Thank you again for this email. Do you think it is possible to >>> use this method for ASL images as well? If so, how would you >>> change the options? >>> >>> Best wishes, >>> >>> Salil Soman, MD, MS >>> >>> On Sat, May 25, 2013 at 11:51 AM, Douglas Greve >>> mailto:gr...@nmr.mgh.harvard.edu>> >>> wrote: >>> >>> >>> On 5/25/13 1:39 PM, Salil Soman wrote: >>> >>>> Thank you Doug. >>>> >>>> Just so I am clear - is the anatomical the nifti T1.mgz or >>>> is it a different file. From your email I gather should do >>>> the following: >>>> >>>> *1) Use bbregister to register the lowb image to the >>>> anatomical. This creates a registration matrix.* >>>> >>>> bbregister -s SUBJECTNAME --mov lowb.nii --initfsl --reg >>>> register.dat >>>> >>> That is right, but add --t2 (since it is t2 weighted). >>> >>>> >>>> *2) Use mri_vol2vol and the registration to map the ADC map >>>> to the anatomical* >>>> mri_vol2vol --mov lowb.nii --targ $vol --inv --interp nearest >>>> --o $vol2diff --reg $outdir/register.dat --no-save-reg >>>> >>> Use the ADC as the moveable (not lowb, but use the lowb for >>> bbregister). The target volume should be the T1.mgz (or any >>> conformed volume). The output will be the adc in the >>> anatomical space (not sure why you call it vol2diff). >>> >>>> *3) use mri_segstats to extract the values* >>>> *mri_segstats* --seg $SUBJECTS_DIR/SUBJECTNAME/mri/wmparc.mgz >>>> --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i lowb.nii --sum >>>> fa.stats >>>> >>> The input would be the adc volume mapped the anatomical >>> space. I would use WMParcStatsLUT.txt or else you'll get a >>> billion different areas not represented in wmparc. You may >>> also want to add "--seg-erode 1" to erode the segmentations >>> by a voxel. This helps to prevent partial voluming. >>> >>> doug >>> >>> >>> Where lowb.nii is the other MRI tissue sequence I am >>>> analyzing (
Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences
6878 6878.0 ctx-rh-superiorfrontal32.7812 20.7192 0.92.92. 106 2029 2313 2313.0 ctx-rh-superiorparietal 38.3312 13.7339 0.76.76. 107 2030 4177 4177.0 ctx-rh-superiortemporal 39.0893 10.6739 9.72.63. 108 2031 2662 2662.0 ctx-rh-supramarginal 39.5586 9.440416.70.54. 109 2032 300 300.0 ctx-rh-frontalpole43.1600 12.4866 8.71.63. 110 2033 1068 1068.0 ctx-rh-temporalpole 32.2996 8.338114.56.42. 111 2034 295 295.0 ctx-rh-transversetemporal 48.2644 8.020233.64.31. 112 2035 2511 2511.0 ctx-rh-insula 38.9263 6.839818.55.37. On Thu, Sep 18, 2014 at 2:05 PM, Douglas N Greve wrote: > > Are you sure that *all* are 0? By passing it FreeSurferColorLUT.txt, you > force it to report hundreds (or thousands) of ROIs which are not > represented in the aparc+aseg.mgz. Also, try removing --seg-erode. > > On 09/18/2014 04:43 PM, Salil Soman wrote: > >> Dear Doug, >> >> Thank you for your email. >> >> The registration overlap looks reasonable. Thank you for considering this >> question. >> >> Best wishes, >> >> Sal >> >> On Thu, Sep 18, 2014 at 12:14 PM, Douglas N Greve < >> gr...@nmr.mgh.harvard.edu <mailto:gr...@nmr.mgh.harvard.edu>> wrote: >> >> >> When you look at SUBJECT_ID_CBF_reg.nii.gz, does it look >> reasonable? Does it overlay correctly on the T1.mgz? >> doug >> >> On 09/14/2014 11:40 PM, Salil Soman wrote: >> >> Thank you Doug. I am having trouble with extracting >> statistics using this method. >> >> I am able to use bbregister to get a transformation that >> registers the PD image of the ASL to the T1. I then used this >> transformation matrix to register the CBF map for the ASL >> study into the T1.mgz space. Checking the images, the >> registration looked reasonable. However, when I try to extract >> the values from the registered image using the vois from >> aparc+aseg.mgz, and the FreeSurferColorLUT I get all 0 values. >> >> *The command I ran is:* >> >> mri_segstats --seg $SUBJECTS_DIR/SUBJECT_ID/mri/aparc+aseg.mgz >> --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i >> SUBJECT_ID_CBF_reg.nii.gz --sum SUBJECT_ID_ASL.stats --seg-erode 1 >> >> *where SUBJECT_ID_CBF_reg.nii.gz was generated by running:* >> >> mri_vol2vol --mov SUBJECT_ID_CBF.nii.gz --targ T1.mgz --interp >> nearest --o SUBJECT_ID_CBF_reg.nii.gz --reg SUBJECT_ID.dat >> --no-save-reg >> >> (and this was run with T1.mgz and SUBJECT_ID_CBF.nii.gz in the >> same folder). >> >> *for which SUBJECT_ID.dat was generated by running the code:* >> >> bbregister --s SUBJECT_ID --mov SUBJECT_ID_ASL_PD.nii.gz --reg >> SUBJECT_ID.dat --t1 --init-fsl >> >> Thank you for your consideration of this question. >> >> Best wishes, >> >> Salil Soman, MD, MS >> >> >> >> >> On Sun, Sep 14, 2014 at 3:32 PM, Douglas Greve >> mailto:gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.edu >> <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: >> >> yep, you can use it for anything. >> doug >> >> >> On 9/14/14 12:52 PM, Salil Soman wrote: >> >> Dear Doug, >> >> Thank you again for this email. Do you think it is >> possible to >> use this method for ASL images as well? If so, how >> would you >> change the options? >> >> Best wishes, >> >> Salil Soman, MD, MS >> >> On Sat, May 25, 2013 at 11:51 AM, Douglas Greve >> > <mailto:gr...@nmr.mgh.harvard.edu> >> <mailto:gr...@nmr.mgh.harvard.edu >> >> <mailto:gr...@nmr.mgh.harvard.edu>>> wrote: >> >> >> On 5/25/13 1:39 PM, Salil Soman wrote: >> >> Thank you Doug. >> >>
Re: [Freesurfer] possible to use freesurfer segmentations to get mean values for anatomic structures from other sequences
Dear Doug, Thank you for your email. On Wed, Sep 24, 2014 at 8:57 AM, Douglas N Greve wrote: > > >> 2) While most of the CBF to T1 registrations using the transformation for >> the PD to the T1 image worked reasonably, there are a few where the >> registration is a little off (almost exclusively requiring some translation >> in the SI direction) - what is the best way to correct the registration and >> generate a better fitting transformation matrix? (either manually or using >> some other tool) >> > What did you use to do the registration? bbregister: bbregister --s $2_FS --mov $2_ASL_PD.nii.gz --reg $2_Reg.dat --t1 --init-fsl > >> 3) Do I not need to use seg-erode to minimize partial voluming? >> > You may, but then you may lose an entire ROI, esp in cortex. I'll have > some PVC software for the next release. Thanks! Will take out erode step with the ASL data. Best wishes, Sal ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] freesurfer gpu acceleration using amd video cards?
Dear List Members, Does anyone know if it is possible to use freesurfer gpu based acceleration using amd video cards? Thanks, Salil Soman, MD, MS ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
[Freesurfer] Problem with overlay of EPI analyze volume over T1 analyze volume in free surfer
Hi, I have been working with an image dataset of EPI images and MR images that have been registered in the freesurfer (transformation for which is stored in a .reg file). A T1 mgz volume was made using the following command: mri_convert -it analyze -ot mgh -i T1001.img -o T1.mgz I formed the EPI volume using the following command: mri_convert -it analyze -ot mgh -i F0001.img -o BH1.mgz when I load the T1 volume, and then overlay the EPI volume in tkmedit, with the reg file for transformation, I get a yellow box superimposed over a T1 image. The EPI volume itself appears to be properly formed, as I can read it directly into freesurfer and get a properly formed image. Was wondering if anyone had any suggestions as to what may be going wrong? Thanks, Salil Soman [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Using overlay in Freesurfer
Can the overlay feature in freesurfer be used to overlay anatomic images? (or does the overlay image have to be spatial data). I'm trying to overlay a EPI image over a T1 image, and the EPI volume is showing up as a yellow block. The EPI and the T1 mgz files were both generated by mri_convert from spm files. Thanks, Salil Soman [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Re: Outputting reformatted images in freesurfer
Hi, I have 2 images loaded into freesurfer (1 as an overlay) with the images transformed using a .reg file. Is there a way in freesurfer to output each of the loaded images in the pose they are in after loading the .reg file? (so the pose of each image is the result of whatever transforms are applied to the images by the .reg file) The end result I'm looking for is that is both images are loaded into freesurfer with a reg file that applies no transforms, the images will be the same as though the original .reg file was used. Thanks, Salil Soman [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Outputting reformatted images in freesurfer
Hi, I have 2 images loaded into freesurfer (1 as an overlay) with the images transformed using a .reg file. Is there a way in freesurfer to output each of the loaded images in the pose they are in after loading the .reg file? (so the pose of each image is the result of whatever transforms are applied to the images by the .reg file) The end result I'm looking for is that is both images are loaded into freesurfer with a reg file that applies no transforms, the images will be the same as though the original .reg file was used. Thanks, Salil Soman [EMAIL PROTECTED] ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] synthstrip error
External Email - Use Caution
Hi,
I am passing synthstrip an nii.gz file, and it keeps giving the error
"ValueError: cannot determine file format from extension for test " (full
error below). Any suggestions on how to fix this issue? The nifti files was
made from dicom images using dcm2nnix.
Thanks!
Salil
Configuring model on the CPU
Running SynthStrip model version 1
Input image read from: test.nii.gz
Traceback (most recent call last):
File "/usr/local/freesurfer/7.3.2//python/scripts/mri_synthstrip", line
245, in
image.save(args.out)
File
"/usr/local/freesurfer/7.3.2/python/lib/python3.8/site-packages/surfa/core/framed.py",
line 274, in save
save_framed_array(self, filename, fmt=fmt)
File
"/usr/local/freesurfer/7.3.2/python/lib/python3.8/site-packages/surfa/io/framed.py",
line 136, in save_framed_array
raise ValueError(f'cannot determine file format from extension for
{filename}')
ValueError: cannot determine file format from extension for test
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