[Freesurfer] Postdoctoral position: the brain connectome in twins populations

Dear brain imaging fellows, One post-doc position is available in our group, the deadline is 30-08-2013. Please find the details below: *** Department Center of Neurodevelopmental Disorders at Karolinska Institutet (KIND) (www.ki.se/kind) KIND is a competence center for

Re: [Freesurfer] How to transfer a reconstructed pial surface file into a 256*256*256 matlab matrix file?

Hi Bruce, Thanks very much for the explanation. According to your suggestion, I think maybe I should try to figure it out with a 2D fast marching process. I could extract it to a 2 dimension matrix by matlab with FreeSurfer package, right? Best, Yunxin 2013/8/6 Bruce Fischl > Hi Yunxin > > co

Re: [Freesurfer] re Annotation2label

Thank you. I also have one question; it says default is "white" surface, but I want measure cortical thickness. Can I leave white in or do I change --surf to gray for this? Kind Wishes, Linn On Tue, Aug 6, 2013 at 6:50 PM, Douglas N Greve wrote: > > Use --annotation aparc.a2009s > Run it with

Re: [Freesurfer] How to transfer a reconstructed pial surface file into a 256*256*256 matlab matrix file?

Hi Yunxin can you explain a bit more about what you are trying to achieve? We already provide a tesselated representation of the pial surface. I don't think it will be possible to discretize it into a volume and retesseelate with a fast marching algorithm without giving up lots of accuracy

[Freesurfer] set message

Hi folks, When issuing a recon-all command, I'm seeing the following message: set: Variable name must contain alphanumeric characters recon-all stalls and doesn't move forward (doesn't even create the subject directory). I'm using Freesurfer 5.3.0 (freesurfer-Linux-centos6_x86_64-stable-pub-v5.

[Freesurfer] mri_cvs_register for EPI

Hello, I'm trying to use mri_cvs_register (whose registration accuracy is, by the way, jaw-dropping) for EPI images. However, the descriptions which I've found on the web do not make the task easier. My goal is to get functional images in cvs_avg35_inMNI152 space, resampled to 3mm isotropic resolu

Re: [Freesurfer] Longitudinal correction of volumes - eTIV

Hi Alex, use the eTIV from the longitudinal subject. In theory, the size of the skull is not changing, and the longitudinal analysis gives you the best estimate of this unchanging number. doug On 08/06/2013 06:00 PM, Alex Hanganu wrote: > Hello, > > I am measuring the changes of subcortical vol

Re: [Freesurfer] set message

what is your command line? On 08/07/2013 10:19 AM, Heather L. Urry wrote: > Hi folks, > > When issuing a recon-all command, I'm seeing the following message: > > set: Variable name must contain alphanumeric characters > > recon-all stalls and doesn't move forward (doesn't even create the > sub

Re: [Freesurfer] Longitudinal correction of volumes - eTIV

Thank you Doug ! Le 7/8 11:44, Douglas N Greve a écrit : > Hi Alex, use the eTIV from the longitudinal subject. In theory, the size > of the skull is not changing, and the longitudinal analysis gives you > the best estimate of this unchanging number. > doug > > On 08/06/2013 06:00 PM, Alex Hanga

[Freesurfer] Tracula question

Hi Anastasia: For one brain I got this error message : csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] : trac-all -prep -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-107 Too many ('s. ERROR: must sp

Re: [Freesurfer] trac-all inquiry

Hi David - Every time you run trac-all, the results get appended to this file, so you need to look for error messages only in the more recent invocation of trac-all. The first error there seems to be: Error: bvecs and bvals don't have the same number of entries Do you have the same n

Re: [Freesurfer] Tracula question

Yes, please attach the dmrirc and trac-all.log. Thanks! a.y On Wed, 7 Aug 2013, Alan Francis wrote: > Hi Anastasia: > > For one brain I got this error message : > > csh::alanf@cerebro > [/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons] > : trac-all -prep > -

Re: [Freesurfer] Validation of results

Hi Doug, I can't visualize the maps on the linux server I'm using but I have the cluster summary files below for DODS and DOSS. As you can see they are quite different. What do you think might be driving the DODS result? I want to look at the difference in surface area between the two genotype gro

Re: [Freesurfer] set message

Here it is: recon-all -i /home/hurry01/r/resdep_mri_data/resdep014/265000-10-1.dcm -s resdep214 -all & (sorry for not thinking to include it originally) Heather On Wed, Aug 7, 2013 at 11:48 AM, Douglas N Greve wrote: > what is your command line? > > > > > On 08/07/2013 10:19 AM, Heather L. Ur

Re: [Freesurfer] set message

and what shell are you using On Wed, 7 Aug 2013, Douglas N Greve wrote: > what is your command line? > > > > > On 08/07/2013 10:19 AM, Heather L. Urry wrote: >> Hi folks, >> >> When issuing a recon-all command, I'm seeing the following message: >> >> set: Variable name must contain alphanumeric ch

Re: [Freesurfer] set message

Ah, sorry-- that too: tcsh 6.18.01. (The command, which I just sent in a previous message, was as follows: recon-all -i /home/hurry01/r/resdep_mri_data/resdep014/265000-10-1.dcm -s resdep214 -all & ) Heather On Wed, Aug 7, 2013 at 12:42 PM, Bruce Fischl wrote: > and what shell are you usin

[Freesurfer] mri_ca_train UCHAR/FLOAT

Hello freesurfers, I am currently attempting to run mri_ca_train to create a .GCA atlas based of off a series of subjects. I am receiving the following error: *** processing subject CMH-3074, 1 of 10... mri_ca_train: segme

Re: [Freesurfer] mri_ca_train UCHAR/FLOAT

yes, mri_convert -odt float will do it. What format is it in? On Wed, 7 Aug 2013, Mark Plantz wrote: Hello freesurfers,    I am currently attempting to run mri_ca_train to create a .GCA atlas based of off a series of subjects. I am receiving the following error:

Re: [Freesurfer] mri_ca_train UCHAR/FLOAT

It is currently in INT format. Thank you. MP On Wed, Aug 7, 2013 at 11:51 AM, Bruce Fischl wrote: > yes, mri_convert -odt float will do it. What format is it in? > > > On Wed, 7 Aug 2013, Mark Plantz wrote: > > Hello freesurfers, >>I am currently attempting to run mri_ca_train to create a

[Freesurfer] 5.3.0 patch

Dear Freesurfer experts, I recently installed the stable 5.3.0 version of Freesurfer (CentOS 4, 64-bit) and encountered the known problem with the missing ribbon.mgz file when running -autorecon1 -autorecon2. I wonder how I can obtain the patch mentioned for this problem in the release notes, an

Re: [Freesurfer] Tracula question

Thank you Anastasia. Another brain had a different problem: Here is the trac-all log: mri_concat --i /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons//106/dmri/dwi_frame.nii.gz --mean --o /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_reco

[Freesurfer] Different results in surface and volume analyses

Hello everyone, I am looking at a visual stimulus vs fixation contrast in my individual subjects' data to make sure we are seeing normal activation there. If I look at the surface data in tksurfer, I see activation in the occipital cortex, but in the mni305 analysis, there is no activation in t

Re: [Freesurfer] Tracula question

Please attach the file trac-all.log. I can't tell what's going on just by looking at the end of it. On Wed, 7 Aug 2013, Alan Francis wrote: Thank you Anastasia. Another brain had a different problem: Here is the trac-all log: mri_concat --i /autofs/space/dali_003/users/BW_project_DTI/FreeS

Re: [Freesurfer] 5.3.0 patch

get mri_segstats from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_segstats then cp mri_segstats $FREESURFER_HOME/bin doug On 08/07/2013 01:09 PM, Moran Cohn wrote: > > Dear Freesurfer experts, > > I recently installed the stable 5.3.0 version of Freesurfer (CentOS 4

Re: [Freesurfer] set message

Ah! That was helpful, Doug. While eliminating the & at the end didn't do anything, running the debug version of the command shows the following at the end of log.txt (attached): set subjdir = $SUBJECTS_DIR/$subjid set subjdir = /home/hurry01/.gvfs/ebblvm$ on callunavm.psy.tufts.edu/projects/resdep

Re: [Freesurfer] hippo_subfields atlas

Hi again! I have another question about the hippocampal subfields atlas--might be a silly one. Is there a way to extract volumes from the mesh collection? Thanks a lot, Raja On Wed, Jul 31, 2013 at 5:06 PM, Juan Eugenio Iglesias < igles...@nmr.mgh.harvard.edu> wrote: > Sounds good, but please

Re: [Freesurfer] Tracula question

Hi Anastasia: Here is the trac-all log. Thanks so much: csh::alanf@cerebro[/autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/106/Diffusion_Recons] : trac-all -prep -c /autofs/space/dali_003/users/BW_project_DTI/FreeSurfer_5.3_Data/diffusion_recons/dmrirc-106 INFO:

Re: [Freesurfer] Tracula question

It looks like there may be something wrong with the bval file. Are you using a different one for this particular subject? On Wed, 7 Aug 2013, Alan Francis wrote: Hi Anastasia: Here is the trac-all log. Thanks so much: csh::alanf@cerebro [/autofs/space/dali_003/users/BW_project_DTI/FreeSur

[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 ro

[Freesurfer] Group analysis

Hi, FreeSurfers. Is it possible to use FreeSurfer's group analysis tools to investigate surface deformation instead of thickness? I guess it would be interesting for subcortical structures like putamen, amygdala or hippocampus. Let's say you get the putamen data from 15 subjects and compare it to p

[Freesurfer] flip hemisphere of manual label

Hi, Is there a way to transpose a manual surface label in fsaverage space onto the contralateral hemisphere? With tksurfer it opens in the opposite hemisphere but it does not correspond to the contralateral region. Thanks in advance. Best, Jonathan ___

[Freesurfer] Curvature, cortical thickness, LGI and artifacts

Hello-- Our dataset has 130ish scans with a bad temporal lobe artifact and a minor parietal lobe artifact. This artifact has affected the normalization and thus the white matter/gray matter selection, which we've manually fixed. However, the temporal lobe artifact is bad enough that chunks of data

Re: [Freesurfer] preferred method for generating appropriate bvecs for tracula

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 v

[Freesurfer] error when using selxavg3-sess in retinotopy analysis

Hi, I followed the steps for doing the retinotopy analysis. At the end I made my analysis as follows: mkanalysis-sess -a Retinotopy_ZY -surface self lh -TR 2 -retinotopy 36 -paradigm rtopy.par -fsd bold -fwhm 5 and then execute selxavg3-sess: selxavg3-sess –a Retinotopy_ZY –s sessi

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?

Re: [Freesurfer] hippo_subfields atlas

Shame on me; there's a way of doing this. You need a reference volume; for the hippocampal subfield atlas: $FREESURFER_HOME/data/GEMS/CurrentMeshCollection30.gz the reference volume would be: $FREESURFER_HOME/data/GEMS/imageDump.mgz The command would be: kvlRasterizeAtlasMesh CurrentMeshCollect

Re: [Freesurfer] hippo_subfields atlas

Thanks very much! On Wed, Aug 7, 2013 at 4:23 PM, Juan Eugenio Iglesias < igles...@nmr.mgh.harvard.edu> wrote: > Shame on me; there's a way of doing this. You need a reference volume; > for the hippocampal subfield atlas: > $FREESURFER_HOME/data/GEMS/CurrentMeshCollection30.gz > the reference v

Re: [Freesurfer] preferred method for generating appropriate bvecs for tracula

Hi Sal - Right now you'd just have to try it on one data set and look at the eigenvectors of the tensor (display dmri/dtifit_V1.nii.gz as lines) to make sure they're pointing in the right way. I'm hoping for the next freesurfer release to finally get mri_convert to read gradient vectors off

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

Re: [Freesurfer] preferred method for generating appropriate bvecs for tracula

Freeview can do this in principle, but the current version of freeview has a known bug with displaying eigenvectors as lines (see known issues in http://surfer.nmr.mgh.harvard.edu/fswiki/ReleaseNotes), so for now you can use fslview. On Wed, 7 Aug 2013, Salil Soman wrote: Thank you for you

Re: [Freesurfer] hippo_subfields atlas

Final question regarding this: what combinations of labels and meshes should I use? Should I do all combinations between labels and positions, matching labels/positions only, etc? How can I tell which meshes correspond to what labels/areas? Thanks for your time, Raja On Wed, Aug 7, 2013 at 4:26

[Freesurfer] (no subject)

Hi Dr. Fischl, I had a couple subjects that failed recon-all. Although the error log said recon-all failed at mri_watershed it looks like the root problem is a couple steps earlier, because the nu.mgz looks too dark. This was discussed in a previous thread from 2008. http://www.mail-archive.com/f

Re: [Freesurfer] error when using selxavg3-sess in retinotopy analysis

It is having problems reading the subjectname file in the session folder. Look in there to see if there is something obviously wrong. Did you create it on a windows computer? doug On 08/07/2013 04:16 PM, Sepide Movaghati wrote: > Hi, > > I followed the steps for doing the retinotopy analysis. A

Re: [Freesurfer] (no subject)

Hi Abid what version of FS are you using? Bruce On Wed, 7 Aug 2013, aqure...@nmr.mgh.harvard.edu wrote: > Hi Dr. Fischl, > > I had a couple subjects that failed recon-all. Although the error log said > recon-all failed at mri_watershed it looks like the root problem is a > couple steps earlier,

Re: [Freesurfer] Different results in surface and volume analyses

Hi Emily, the processing stream is designed to mask out cortical regions from the volume analysis. The volume analysis is used for subcortical structures. To make sure that the same voxels are not analyzed twice, the cortical surface is masked out of the mni305 analysis. doug ps. If you really

Re: [Freesurfer] Group analysis

Hi Marcos, we're not really set up to do this kind of thing. The subcortical structures in fsaverage are not appropriate for surface-based analysis. We do not generate surface for subcortical structures from individuals. I think FSL might do this kind of thing. doug On 08/07/2013 04:03 PM,

Re: [Freesurfer] trac-all inquiry

Hi - further to my prior email find attached please a clean version of the log file - without the append of  previous attempts as you can see there are no errors in the log although as i said the last line in the Terminal said Segmentation fault (core dumped) cheers ds http://www1.imperial.ac.uk/me