[Freesurfer] claustrum segmentation
Hi freesurfer experts, I have a few questions on claustra segmentations. I tried to look into archives but did not find an answer to all my points so far.. I have a group of subjects in which I would like to segment claustrum. Looking at lookup table a color is assignied for both left and right claustra; however, after running segmentation, I opened aparc+aseg results and did not find claustra. My questions are: 1) Results of aparc+aseg.mgz are different from aparc.a2009s+aseg ones; which one does correspond to *Desikan-Killiany *and which one to *Destrieux*? I mean, looking at tutorials, aparc.a2009+aseg should correspond to Destrieux, but I could not find aparc.DKTlas40+aseg, thus I am not sure about naming conventions... 2) Do both atlases in principle permit to segment claustrum? In this case, would missing of claustra be due to poor quality of my data? how could I work on processing pipeline to improve my parcellation and thus obtaining claustra? 3) If claustrum is not automatically segmented, would you please provide some hints on how to add a new structure based on manual segmentations and include them in segmentation pipeline? Any suggestion will be appreciated. Best Regards, Alessandro ___ 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] FW: problem with hard coded directory (/scratch)
Hi Douglas, You asked us to give you an example of the problem program. I will try to do it here, but if it is not what you want, please let me know. we ran recon-all -all -s -hippocampal-subfields-T1T2 . We saw the program tried to create /scratch/$subject_hippoSF_T1_v10_right directory and failing with (Read-only file system) because the user does not have permission to write to /scratch. I can also send you the strace output if needed. Thank you! - Message: 4 Date: Mon, 4 Jan 2016 13:37:48 -0500 From: Douglas N Greve Subject: Re: [Freesurfer] FW: problem with hard coded directory (/scratch) To: freesurfer@nmr.mgh.harvard.edu Message-ID: <568abbfc.5000...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed Can you give us specific examples of problem programs? On 01/04/2016 09:54 AM, Fengji Geng wrote: > Hello Bruce, > > Happy New Year! > > After we reported the error related to '/scratch' several weeks ago > (see the email attached below), we tested the newest version of > freesurfer 6.0 recently, it looks likes that a lot of "if (-e > /scratch)" have been changed to "if (-dw /scratch)". However, there > are still a lot of binaries in the bin directory that match the string > "scratch", which cause the same error that I encountered before. I am > wondering if it is possible for you to fix '/scratch' in the bin > directory. > > Thank you! - Fengji ___ 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] MPRAGE Data
Hi Scott we are almost certainly not allowed to do so either. Is this Siemens data? Why do you have raw data? Is it just this one dataset or do you need to process raw data more often? cheers Bruce On Wed, 6 Jan 2016, Scott E wrote: > Hi folks, > Hopefully I'm not asking this question in the wrong place -- please let me > know if I am! > > I have a T1 MPRAGE data file which I'm trying to process into images. I > can't, however, figure out how this data is organized within the file. The > manufacturer can't provide me details of how to decode the data without a > research agreement, and as I don't own the MRI machine itself, I cannot > enter into such an agreement. > > Does anyone have experience decoding raw MPRAGE data? > > Thanks! > Scott > [f18dQhb0S7ks8dDMPbW2n0x6l2B9gXrN7sKj6v5dlMTN1qwdsgdVn4qN8qlRZ4d3_yKW8S5dZm > 1k1H6H0?si=5684348013772800&pi=2e8d56bc-2c0e-473e-b487-a6a6d4ffde35] > > ___ 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] FW: problem with hard coded directory (/scratch)
can you be more specific? Which program failed? Also, please send us the recon-all.log file so we have the information we need to help you. cheers Bruce On Thu, 7 Jan 2016, Fengji Geng wrote: Hi Douglas, You asked us to give you an example of the problem program. I will try to do it here, but if it is not what you want, please let me know. we ran recon-all -all -s -hippocampal-subfields-T1T2 . We saw the program tried to create /scratch/$subject_hippoSF_T1_v10_right directory and failing with (Read-only file system) because the user does not have permission to write to /scratch. I can also send you the strace output if needed. Thank you! --- -- Message: 4 Date: Mon, 4 Jan 2016 13:37:48 -0500 From: Douglas N Greve Subject: Re: [Freesurfer] FW: problem with hard coded directory (/scratch) To: freesurfer@nmr.mgh.harvard.edu Message-ID: <568abbfc.5000...@nmr.mgh.harvard.edu> Content-Type: text/plain; charset=windows-1252; format=flowed Can you give us specific examples of problem programs? On 01/04/2016 09:54 AM, Fengji Geng wrote: > Hello Bruce, > > Happy New Year! > > After we reported the error related to '/scratch' several weeks ago > (see the email attached below), we tested the newest version of > freesurfer 6.0 recently, it looks likes that a lot of "if (-e > /scratch)" have been changed to "if (-dw /scratch)". However, there > are still a lot of binaries in the bin directory that match the string > "scratch", which cause the same error that I encountered before. I am > wondering if it is possible for you to fix '/scratch' in the bin > directory. > > Thank you! - Fengji ___ 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] Recon-all get stucked without error during processing
Hi Bruce, This problem isn't resolved yet. I uploaded the subject raw 3D T1 on FileDrop. Changing the watershed parameters could be done in the recon-all command ? Thanks in advance ! Best regards, Matthieu 2016-01-07 14:58 GMT+01:00 Bruce Fischl : > Hi Matthieu > > was this ever resolved? If not, you can upload the subject and we will > take a look. You could also try messing with the watershed parameters > (starting with changing the preflooding height to me more aggressive). > > cheers > Bruce > > > > On Thu, 10 Dec 2015, Matthieu Vanhoutte wrote: > > Hi Bruce, >> >> Do you have an idea of how to solve this problem of skull stripping >> (below) >> ? >> >> Best regards, >> Matthieu >> >> 2015-12-09 16:25 GMT+01:00 Matthieu Vanhoutte < >> matthieuvanhou...@gmail.com>: >> Hi Bruce, >> >> In fact T1.mgz is ok, but the skull stripping failed and seemed to >> have taken only the jawbone and the neck. >> >> Best regards, >> Matthieu >> >> 2015-12-09 16:16 GMT+01:00 Bruce Fischl : >> Hi Matthieu >> >> you need to track backwards and see where the problem >> started. Why is the norm warped? Actaully, it shouldn't be >> warped, although it might be truncated if the skull >> stripping failed. >> >> cheers >> Bruce >> On Wed, 9 Dec 2015, Matthieu Vanhoutte wrote: >> >> Hi Bruce, >> >> Indeed norm.mgz isn't empty but doesn't look >> well (truncated and warped). >> >> Is this bug fixed in the v6 beta release ? >> >> If this is the case : >> 1) Would you advise me to try on the v6 ? >> 2) Should I so relaunch all recon-all process >> on my subjects computed with v5.3 and work >> only with the v6 beta ? >> >> Best regards, >> Matthieu >> >> 2015-12-09 15:55 GMT+01:00 Bruce Fischl >> : >> Hi Matthieu >> >> this might be a bug that is fixed in >> 6.0. Can you cehck the input to >> mri_cc (norm.mgz) and make sure it is >> not empty? In older versions if the >> skull stripping failed and generated an >> empty >> norm.mgz/aseg.auto_noCCseg.mgz the >> mri_cc code would hang. >> >> cheers >> Bruce >> >> On Wed, 9 Dec 2015, >> Matthieu Vanhoutte wrote: >> >> > Dear FS epxerts, >> > >> > I have launched a recon-all process on >> a subject. Unfortunately, I tried two times >> but the process get stucked at >> the same step >> > without error. >> > >> > Please found the recon-all.log >> associated attached to this mail. >> > >> > Thanks in advance for helping ! >> > >> > Best regards, >> > Matthieu >> > >> > >> ___ >> 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 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 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 c
[Freesurfer] R: Re: FDR correction
Thanks.
- on question 2:
I have run
rh = MRIread('sig.mgh');
but this error occur
Undefined function 'MRIread' for input arguments of type 'char'.
no help is permitted on MRIread
-on question 3:
I'm using this command line to visualize the map describing the functional
connectivity form seed to cortex
tksurfer fsaverage rh inflated -aparc -overlay R_seed/my-glm.wls/group.
diff/sig.nii.gz -fminmax 1.3 3
tksurfer fsaverage lh inflated -aparc -overlay L_seed/my-glm.wls/group.
diff/sig.nii.gz -fminmax 1.3 3
in this way I visualize correctly for right and left hemisphere the
connectivity from ipsilateral seed.
If I would visualize the the connectivity from contralateral seed, how can I
do?
If I use
tksurfer fsaverage lh inflated -aparc -overlay R_seed/my-glm.wls/group.
diff/sig.nii.gz -fminmax 1.3 3
tksurfer fsaverage rh inflated -aparc -overlay L_seed/my-glm.wls/group.
diff/sig.nii.gz -fminmax 1.3 3t
-on question 4:
I have resolved with this command line:
mri_surfcluster --in sig.nii.gz --hemi rh --sign abs --no-adjust --fdr 0.05 --
minarea 5 --sum summaryfile --subject fsaverage --annot aparc
but I have difficulty to undestand which is the option to visualize the map
corrected by mri_surfcluster.
Additionally, from --help I do not understand the use of --ocn and --cst
options.
Best regards,
Stefano
>Messaggio originale
>Da: gr...@nmr.mgh.harvard.edu
>Data: 7-gen-2016 0.34
>A:
>Ogg: Re: [Freesurfer] FDR correction
>
>
>
>On 01/06/2016 11:00 AM, std...@virgilio.it wrote:
>> Hi list,
>>
>> I would like to ask you a number of questions regarding the FDR which
>> is performed following seed-based fcMRI using FS-FAST.
>> 1-In the previous mail you have suggested me to use mir_fdr command
>> line (version 6.0). Because I have some problem with new version
>> license (as reported in previous mail) and, overall I have run my data
>> using version 5.3, I would ask you whether FDR integrated in tksurfer
>> (version 5.3) is however reliable as the FDR included in 6.0?
>Yes, they call the same code.
>>
>> 2-Becouse the FDR analysis was performed separately for the right and
>> left hemispheres and the subcortical structures, should I set the FDR
>> threshold to 0.05/3 in order to correct for multiple comparison? (I
>> have one group)
>I'm not sure. You can try to run both hemispheres in matlab, somethiing like
>lh = MRIread('sig.lh.mgh');
>lhp = 10^-abs(lh.vol);
>rh = MRIread('sig.rh.mgh');
>rlhp = 10^-abs(rh.vol);
>
>p = [lhp rhp];
>fdrthresh = fast_fdrthresh(p,fdr);
>
>>
>> 3- Is easy for me to follow the guidelines and visualize the cortical
>> areas which are functionally connected with the omolateral seed. How
>> can I do to visualize also the the cortical areas which are
>> functionally connected with the controlateral seed? If change only the
>> rh/lh in command line the visualization of the results is wrong.
>I don't understand.
>>
>> 4- I'd like to perform mri_surfcluster on a group to eliminate cluster
>> < 5
>> voxels from sig.nii.gz after FDR correction. I'm running
>> mri_surfcluster --in
>> sig.nii.gz --hemi rh --sign abs --fdr 0.05 --minarea 5 --sum
>> summaryfile --ocn
>> ocnid
>> but --subject ... must be included.
>> How should do I do? I would like to run my analysis on group results,
>> not on a single subject.
>If this is from a group analysis, the subject is probablly fsaverage
>>
>> Thanks for your work.
>> Regards,
>>
>>
>> Stefano
>>
>>
>>
>> ___
>> Freesurfer mailing list
>> Freesurfer@nmr.mgh.harvard.edu
>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>--
>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
>FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
>www.nmr.mgh.harvard.edu/facility/filedrop/index.html
>Outgoing: 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.
>
>
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] MPRAGE Data
Hi Bruce, Thanks for your response. I'm writing software that involves processing the data; currently I have one sample set but expect to be working with more in future. Scott > On Jan 7, 2016, at 6:45 AM, Bruce Fischl wrote: > > Hi Scott > > we are almost certainly not allowed to do so either. Is this Siemens data? > Why do you have raw data? Is it just this one dataset or do you need to > process raw data more often? > > cheers > Bruce > > >> On Wed, 6 Jan 2016, Scott E wrote: >> >> Hi folks, >> Hopefully I'm not asking this question in the wrong place -- please let me >> know if I am! >> >> I have a T1 MPRAGE data file which I'm trying to process into images. I >> can't, however, figure out how this data is organized within the file. The >> manufacturer can't provide me details of how to decode the data without a >> research agreement, and as I don't own the MRI machine itself, I cannot >> enter into such an agreement. >> >> Does anyone have experience decoding raw MPRAGE data? >> >> Thanks! >> Scott >> [f18dQhb0S7ks8dDMPbW2n0x6l2B9gXrN7sKj6v5dlMTN1qwdsgdVn4qN8qlRZ4d3_yKW8S5dZm >> 1k1H6H0?si=5684348013772800&pi=2e8d56bc-2c0e-473e-b487-a6a6d4ffde35] > ___ > 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Recon-all get stucked without error during processing
try specifying -no-wsgcaatlas or -no-wsatlas and rerunning just the skull stripping and see if it fixes things cheers Bruce On Thu, 7 Jan 2016, Matthieu Vanhoutte wrote: Hi Bruce, This problem isn't resolved yet. I uploaded the subject raw 3D T1 on FileDrop. Changing the watershed parameters could be done in the recon-all command ? Thanks in advance ! Best regards, Matthieu 2016-01-07 14:58 GMT+01:00 Bruce Fischl : Hi Matthieu was this ever resolved? If not, you can upload the subject and we will take a look. You could also try messing with the watershed parameters (starting with changing the preflooding height to me more aggressive). cheers Bruce On Thu, 10 Dec 2015, Matthieu Vanhoutte wrote: Hi Bruce, Do you have an idea of how to solve this problem of skull stripping (below) ? Best regards, Matthieu 2015-12-09 16:25 GMT+01:00 Matthieu Vanhoutte : Hi Bruce, In fact T1.mgz is ok, but the skull stripping failed and seemed to have taken only the jawbone and the neck. Best regards, Matthieu 2015-12-09 16:16 GMT+01:00 Bruce Fischl : Hi Matthieu you need to track backwards and see where the problem started. Why is the norm warped? Actaully, it shouldn't be warped, although it might be truncated if the skull stripping failed. cheers Bruce On Wed, 9 Dec 2015, Matthieu Vanhoutte wrote: Hi Bruce, Indeed norm.mgz isn't empty but doesn't look well (truncated and warped). Is this bug fixed in the v6 beta release ? If this is the case : 1) Would you advise me to try on the v6 ? 2) Should I so relaunch all recon-all process on my subjects computed with v5.3 and work only with the v6 beta ? Best regards, Matthieu 2015-12-09 15:55 GMT+01:00 Bruce Fischl : Hi Matthieu this might be a bug that is fixed in 6.0. Can you cehck the input to mri_cc (norm.mgz) and make sure it is not empty? In older versions if the skull stripping failed and generated an empty norm.mgz/aseg.auto_noCCseg.mgz the mri_cc code would hang. cheers Bruce On Wed, 9 Dec 2015, Matthieu Vanhoutte wrote: > Dear FS epxerts, > > I have launched a recon-all process on a subject. Unfortunately, I tried two times but the process get stucked at the same step > without error. > > Please found the recon-all.log associated attached to this mail. > > Thanks in advance for helping ! > > Best regards, > Matthieu > > ___ 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
Re: [Freesurfer] MPRAGE Data
I see. Is there a reason it has to be raw data? If it is Siemens we have code for processing it, but I'm pretty sure we aren't allowed to distribute it (is that correct Andre?). If it was a one-time thing you could send it to us, we could convert it and then send it back, but of course that won't work if you are developing a pipeline Bruce On Thu, 7 Jan 2016, Scott Edgar wrote: > Hi Bruce, > > Thanks for your response. > > I'm writing software that involves processing the data; currently I have > one sample set but expect to be working with more in future. > > Scott > >> On Jan 7, 2016, at 6:45 AM, Bruce Fischl wrote: >> >> Hi Scott >> >> we are almost certainly not allowed to do so either. Is this Siemens data? >> Why do you have raw data? Is it just this one dataset or do you need to >> process raw data more often? >> >> cheers >> Bruce >> >> >>> On Wed, 6 Jan 2016, Scott E wrote: >>> >>> Hi folks, >>> Hopefully I'm not asking this question in the wrong place -- please let me >>> know if I am! >>> >>> I have a T1 MPRAGE data file which I'm trying to process into images. I >>> can't, however, figure out how this data is organized within the file. The >>> manufacturer can't provide me details of how to decode the data without a >>> research agreement, and as I don't own the MRI machine itself, I cannot >>> enter into such an agreement. >>> >>> Does anyone have experience decoding raw MPRAGE data? >>> >>> Thanks! >>> Scott >>> [f18dQhb0S7ks8dDMPbW2n0x6l2B9gXrN7sKj6v5dlMTN1qwdsgdVn4qN8qlRZ4d3_yKW8S5dZm >>> 1k1H6H0?si=5684348013772800&pi=2e8d56bc-2c0e-473e-b487-a6a6d4ffde35] >> ___ >> 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 mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] searchable Destrieux atlas by recon all labels?
Is there any interactive or searchable version of the Destrieux atlas parcellations (the ones used by aparc.a2009s.annot)? It would be very helpful to be able to toggle back and forth between individual recon-all labels and a color atlas of the relevant region when examining ROI-based quantitative output (output that is not visual). Thanks, Andrea B. ___ 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] searchable Destrieux atlas by recon all labels?
Hi Andrea I'm not sure what you mean but I'm pretty certain the answer is "no". sorry Bruce On Thu, 7 Jan 2016, Andrea Bozoki wrote: Is there any interactive or searchable version of the Destrieux atlas parcellations (the ones used by aparc.a2009s.annot)? It would be very helpful to be able to toggle back and forth between individual recon-all labels and a color atlas of the relevant region when examining ROI-based quantitative output (output that is not visual). Thanks, Andrea B. ___ 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] Mask out medial wall?
Hi, Is there a way to mask out the medial wall in the tksurfer command? I’m looking for a way to have the map visually look as if there’s simply no activation within the medial wall (showing a plain gray striped/curvature shown brain in that area instead), as opposed to having the medial wall be a different color or just not there/hole in the brain. Best, Stephanie Stephanie N. DeCross Clinical Research Coordinator Psychiatric Neuroimaging Research Program Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, Charlestown, MA 02129 Phone: 617-724-3283 Fax: 617-726-4078 ___ 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] Mask out medial wall?
Hi Stephanie in tksurfer I think you can type: mask_label lh.cortex (or rh.cortex) at the tcl (%) command line cheers Bruce On Thu, 7 Jan 2016, DeCross, Stephanie N. wrote: Hi, Is there a way to mask out the medial wall in the tksurfer command? I’m looking for a way to have the map visually look as if there’s simply no activation within the medial wall (showing a plain gray striped/curvature shown brain in that area instead), as opposed to having the medial wall be a different color or just not there/hole in the brain. Best, Stephanie Stephanie N. DeCross Clinical Research Coordinator Psychiatric Neuroimaging Research Program Martinos Center for Biomedical Imaging Massachusetts General Hospital 149 13th Street, Charlestown, MA 02129 Phone: 617-724-3283 Fax: 617-726-4078 ___ 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] searchable Destrieux atlas by recon all labels?
freeview partial solution If this is important to you, you could write a quick script to do this for you: 1. mri_annotation2label to output all labels 2. write a script to launch freeview and load all of the labels (reading the color and applying it from the FS ctab file) e.g. freeview -f surf/lh.inflated:label=label/lh.BA1.label:label_color=255,0,0 & 3 you could then scroll through and click all of them off, and then click to load each one individually. or perhaps a new option could be added to the surface label called :label_opacity=0 (which would uncheck the view label option). hth d On Thu, Jan 7, 2016 at 3:53 PM, Bruce Fischl wrote: > Hi Andrea > > I'm not sure what you mean but I'm pretty certain the answer is "no". > > sorry > Bruce > > On Thu, 7 Jan 2016, Andrea Bozoki wrote: > >> Is there any interactive or searchable version of the Destrieux atlas >> parcellations (the ones used by aparc.a2009s.annot)? >> >> It would be very helpful to be able to toggle back and forth between >> individual recon-all labels and a color atlas of the relevant region when >> examining ROI-based quantitative output (output that is not visual). >> >> >> >> Thanks, >> >> Andrea B. >> >> >> >> > > ___ > 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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FW: problem with hard coded directory (/scratch)
Do you have the problem if you do not include the hippo subfields? On 01/07/2016 08:15 AM, Fengji Geng wrote: > Hi Douglas, > You asked us to give you an example of the problem program. I will try > to do it here, but if it is not what you want, please let me know. > > we ran recon-all -all -s -hippocampal-subfields-T1T2 > . We saw the program tried > to create /scratch/$subject_hippoSF_T1_v10_right directory > and failing with (Read-only file system) because the user does not > have permission to write to /scratch. > > I can also send you the strace output if needed. > > Thank you! > > - > Message: 4 > Date: Mon, 4 Jan 2016 13:37:48 -0500 > From: Douglas N Greve > Subject: Re: [Freesurfer] FW: problem with hard coded directory > (/scratch) > To: freesurfer@nmr.mgh.harvard.edu > Message-ID: <568abbfc.5000...@nmr.mgh.harvard.edu> > Content-Type: text/plain; charset=windows-1252; format=flowed > > Can you give us specific examples of problem programs? > > On 01/04/2016 09:54 AM, Fengji Geng wrote: > > Hello Bruce, > > > > Happy New Year! > > > > After we reported the error related to '/scratch' several weeks ago > > (see the email attached below), we tested the newest version of > > freesurfer 6.0 recently, it looks likes that a lot of "if (-e > > /scratch)" have been changed to "if (-dw /scratch)". However, there > > are still a lot of binaries in the bin directory that match the string > > "scratch", which cause the same error that I encountered before. I am > > wondering if it is possible for you to fix '/scratch' in the bin > > directory. > > > > Thank you! > > - > Fengji > > > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- 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 FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: 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.
[Freesurfer] PET processing seg fault with mri_glmfit --mrtm1
Hi Freesurfer developers, I’m trying to perform BP analysis with mri_glmfit —mrtm1. I ran mri_gtmpvc without PVC, which finished without error. However, the km.hb.tac.nii.gz appears empty when I open it with fslview or tkmedit, although this may be due to the nature of the file (I’m not sure what it is supposed to show). The km.ref.tac.dat and km.hb.tac.dat are normal. Please let me know what you think. The command and error: mri_glmfit --y km.hb.tac.nii.gz --mrtm1 km.ref.tac.dat time.dat --o mrtm1 --no-est-fwhm --nii.gz Segmentation fault (core dumped) Where time.dat is a text file with the time (in seconds) of each frame: 0 30 60 90 120 150 180 240 300 360 420 540 660 780 900 1020 1140 1260 1380 1620 1860 2100 2400 2700 3000 3300 I’m using the linux version 6 beta downloaded on Oct. 30th freesurfer-Linux-centos4_x86_64-dev-20151030 Best, Jonathan ___ 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.
