Freesurfer October 2020

freesurfer@nmr.mgh.harvard.edu

112 participants
180 discussions

Corticalwhitemattervol versus Cerebralwhitemattervol
by Stephanie K 30 Oct '20

30 Oct '20

External Email - Use Caution *Hi all,* *I'm performing an analysis and I want to look at total white matter volume across various cohorts as an outcome. In most of my cohorts, I find the variable CerebralWhiteMatterVol but in one cohort I cannot find this variable, but I am able to find a variable called CorticalWhiteMatterVol. I am planning to perform a meta-analysis analysis across cohorts. Are these two ("CerebralWhiteMatterVol " and "CorticalWhiteMatterVol" measuring the same thing? I have been advised that the change in labels is due to that cohort using Freesurfer v5.30, that it is measuring the same thing but it may or may not be using a different algorithm. Can I meta-analyse corticalwhitemattervol from one cohort with cerebralwhitemattervol from another cohort?Furthermore, in regression analyses, is it the norm to adjust these for estimated intracranial volume?Sorry, if this is a simple question but neuroanatomy is not my field. I would really appreciate your advice.* Many thanks, Roxanna

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preproc-sess error with FreeSurfer 7.1
by Peled, Noam 30 Oct '20

30 Oct '20

Dear FreeSurfer experts! We are running FsFast pipeline to analysis our language task for epilepsy patients. Usually we are using FreeSurfer 5.3. We want to use a newer version, so I decided to jump right to 7.1 (dev) When trying to run preproc-sess -surface {trg_subject} lhrh -s {subject} -fwhm {fwhm} -fsd {fsd} -mni305 -per-run -stc siemens I got the following error: mri_info --nslices --o /autofs/space/megraid_clinical/MEG-MRI/seder/freesurfer/nmr01415/sycabs/005/tmp.110620/nslices.dat /autofs/space/megraid_clinical/MEG-MRI/seder/freesurfer/nmr01415/sycabs/005/fmcpr.nii.gz nslices = 44 slicedelay --nslices 44 --siemens --o /autofs/space/megraid_clinical/MEG-MRI/seder/freesurfer/nmr01415/sycabs/005/tmp.110620/sdf.txt --ngroups 1 File "/usr/local/freesurfer/dev/bin/slicedelay", line 9 print "USAGE: slicedelay --help"; ^ SyntaxError: Missing parentheses in call to 'print' When I reran the same pipeline with FreeSurfer 5.3, it seems to work. Is it a bug in 7.1? Or should we change something in the call? Thanks, Noam

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Re: [Freesurfer] preproc-sess error with FreeSurfer 7.1
by fsbuild 29 Oct '20

29 Oct '20

External Email - Use Caution Hello Noam, The python script /usr/local/freesurfer/dev/bin/slicedelay needs to be run with a version of python that is 2.X, i.e., $ file /usr/local/freesurfer/dev/bin/slicedelay/usr/local/freesurfer/dev/bin/slicedelay: Python script, ASCII text executable $ which python2/bin/python2$ python2 /usr/local/freesurfer/dev/bin/slicedelay --helpUSAGE: slicedelay --help  --o slicedelayfile  --nslices nslices : total number of slices in the volume  --order order (up,down,odd,even,siemens)  --ngroups ngroups (number of slice groups for SMS) Creates an FSL custom slice delay file for use with slicetimer (--tcustom=sdfile).It has a single column of values, one for each slice. Each value is the slice delaymeasured as a fraction of the TR and range from +0.5 (beginning of the TR) to -0.5 (end of the TR). Used for slice-time correction of fMRI. $ which python3/space/freesurfer/python/linux/bin/python3$ python3 /usr/local/freesurfer/dev/bin/slicedelay --help  File "/usr/local/freesurfer/dev/bin/slicedelay", line 9    print "USAGE: slicedelay --help";                                   ^SyntaxError: Missing parentheses in call to 'print'. Did you mean print("USAGE: slicedelay --help")? So I think that means that for you,$ which python- is going to return a python from your PATH such that typing the command “python —version” will report it is rev 3.X and not 2.X. You can try setting the PATH environment variable such that the first python program found in PATH reports it is version 2.X. - R.. On Oct 29, 2020, at 20:47, Peled, Noam <NPELED(a)mgh.harvard.edu> wrote:/usr/local/freesurfer/dev/bin/slicedelay

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Linear Mixed Effects Sample Data Set
by Claire Ciampa 29 Oct '20

29 Oct '20

External Email - Use Caution Hello, I have been following the LME tutorial on the FreeSurfer website, but when I click on the link for the optional sample data set, I get the following error: This site can’t be reached The webpage at *ftp://surfer.nmr.mgh.harvard.edu/pub/data/long_mixed_effects_tools-data.tar.gz <ftp://surfer.nmr.mgh.harvard.edu/pub/data/long_mixed_effects_tools-data.tar…>* might be temporarily down or it may have moved permanently to a new web address. Would it be possible to send me the data set? Thank you, Claire Ciampa

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Extract Area from ROI
by Hua, Jessica 29 Oct '20

29 Oct '20

External Email - Use Caution Hi FreeSurfer Experts, I am tryinig to extract area from a volume-defined ROI. I used code from the FreeSurfer websiite (https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness) to extract thickness, but I was not able to extract area. Here is my code for thickness: mri_surf2surf --s ../../sub-004_session1 --trgsubject ../../fsaverage --hemi lh --sval lh.thickness --tval lh.thickness.fsaverage.mgh mri_segstats --seg $SUBJECTS_DIR/../../fsaverage/label/lh.fsaverage.MFGbin.mgh --in lh.thickness.fsaverage.mgh --sum segstats-lh.thickness.MFGbin.txt How do I modify to extract area? Thank you! Jessica

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Re: [Freesurfer] Please help me. I am such with this for too long!
by Basavaraju, Rakshathi 28 Oct '20

28 Oct '20

External Email - Use Caution Dear Doug, Unfortunately I don't see your response to my email though there is a Re:"my subject" at the beginning. Get Outlook for iOS<https://aka.ms/o0ukef> ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu <freesurfer-bounces(a)nmr.mgh.harvard.edu> on behalf of freesurfer-request(a)nmr.mgh.harvard.edu <freesurfer-request(a)nmr.mgh.harvard.edu> Sent: Tuesday, October 27, 2020 6:48:06 PM To: freesurfer(a)nmr.mgh.harvard.edu <freesurfer(a)nmr.mgh.harvard.edu> Subject: [EXTERNAL] Freesurfer Digest, Vol 200, Issue 55 Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e… or, via email, send a message with subject or body 'help' to freesurfer-request(a)nmr.mgh.harvard.edu You can reach the person managing the list at freesurfer-owner(a)nmr.mgh.harvard.edu When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. Re: Convert FSL .nii ROI into FreeSurfer Label (Douglas N. Greve) 2. Re: Fwd: Freesurfer edits (Douglas N. Greve) 3. Re: Please help me. Stuck with this for too long!!! (Douglas N. Greve) 4. Re: question about PETSurfer (Douglas N. Greve) 5. Re: Issues with Surface segmentation (Sierra Ann R. Jarvis) ---------------------------------------------------------------------- Message: 1 Date: Tue, 27 Oct 2020 18:05:37 -0400 From: "Douglas N. Greve" <dgreve(a)mgh.harvard.edu> Subject: Re: [Freesurfer] Convert FSL .nii ROI into FreeSurfer Label To: <freesurfer(a)nmr.mgh.harvard.edu> Message-ID: <6b459e19-c830-eda7-d365-484a77ca334b(a)mgh.harvard.edu> Content-Type: text/plain; charset="windows-1252" A surface label or a volume label? On 10/25/2020 2:17 PM, Hua, Jessica wrote: > > ????????External Email - Use Caution > > Hi FreeSurfer Experts, > > How can I convert a .nii ROI into a FreeSurfer label? I was able to > convert the .nii into a .mgh file but could not figure out how to > convert to a label file. > > Thank you, > > Jessica > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://urldefense.proofpoint.com/v2/url?u=https-3A__mail.nmr.mgh.harvard.e…

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Problem with pial and white matter segmentation
by Edoardo Pinzuti 28 Oct '20

28 Oct '20

External Email - Use Caution Dear Freesurfer team, I am having trouble with the pial and white matter segmentation of one subject (you can see the picture attached), I tried to set control points but it did not work completely. The segmentation looks not good at all for some slices, do you know what I could do ? Thanks Edoardo

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Issues with Surface segmentation
by Sierra Ann Jarvis 27 Oct '20

27 Oct '20

External Email - Use Caution Hello FreeSurfer Developers, I am attempting to run this subject through a longitudinal process. I have successfully ran and edited the cross-sectional and the .base. My problem occurs when I run the .longs. I do not receive an error in the recon-all.log, but the surfaces on the image when I pull it up on FreeView are very jumbled. Below I have attached a screenshot of a coronal slice to give you an idea of what I am dealing with. I ran the subject through: recon-all -long sub_post/ sub.base -all FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c Recon-all log last line: recon-all -s sub-5504_post.long.sub-5504.base finished without error at Fri Oct 16 13:44:10 MDT 2020 Thank you for your time, Sierra Jarvis

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question about PETSurfer
by 蒋袁芳 27 Oct '20

27 Oct '20

External Email - Use Caution Hello Freesurfer Developers, I have some questions about why the first step of PETSurfer needs to create gtmseg.mgz segmentation. I noticed that the differences between gtmseg.mgz and aseg.mgz are the gtmseg.mgz has a higher resolution and also to separate the pons and the vermis from the brainstem and the cerebellar. I would like to know whether the reason to create the gtmseg.mgz segmentation is because the ROI is based on the Pons? If so, I also have read some other articles that the ROI is based in other regions. Why does the Freesurfer choose Pons instead? Also, what is the purpose of separating the vermis from the cerebellar? Is the reason to create the gtmseg.mgz segmentation just for the system to run the PVC? looking forward to your reply.

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Please help me. Stuck with this for too long!!!
by Basavaraju, Rakshathi 27 Oct '20

27 Oct '20

External Email - Use Caution Dear Freesurfer team, I have been trying to extract local gyrification index in a dataset according to a label which I have created. 1) First of all, I extracted lGI as per DKT areas, which one is lGI value in the ?h.pial_lgi.stats file (derived on running a lGI recon?) # ColHeaders StructName NumVert SurfArea GrayVol ThickAvg ThickStd MeanCurv GausCurv FoldInd CurvInd caudalanteriorcingulate 1094 774 2285 3.234 0.889 0.129 0.031 15 1.3 Is the lGI of caudal anterior cingulate 3.234 or 1.3? 2) I could register a label which I have created to the surface of individual subjects using mrilabel2label which ran alright, and I could view the label on the surface of the individual subject intact on freeview. But after that I am unable to extract lGI value from the designated label only using mris_anatomicalstats. I used the following command: mris_anatomical_stats -l label/outlabelbase-0001.label -f stats/occipital_lGI.stats FS6-LGI-05-Feb-2020_schiz018_G1_MPRAGE rh pial_lgi This throws the error: #MRISread: file '/mnt/share/projects/provenzano/Human/CHR_Rakshathi/LGI/FS6-LGI-05-Feb-2020_schiz018_G1_MPRAGE/surf/rh.pial_lgi' has many more faces than vertices! Probably trying to use a scalar data file as a surface! Then I converted rh_pial.lgi to rh_pial.lgi.asc: mris_convert -c rh.pial_lgi rh.white rh.pial_lgi.asc and then ran: mris_anatomical_stats -l label/outlabelbase-0001.label -f stats/occipital_lGI.stats FS6-LGI-05-Feb-2020_schiz018_G1_MPRAGE rh pial_lgi.asc then the error: Segmentation fault (core dumped) Kindly help me, this analysis is way overdue, and it is seeming like an endless tunnel only of new errors.... Dr. Rakshathi Basavaraju (MD Psychiatry) Postdoctoral Research Scientist Taub Institute for Research on Alzheimer's Disease and the Aging Brain Columbia University Medical Centre 622 West, 168th Street, New York - 10032 E-Mail: rb3419(a)cumc.columbia.edu<mailto:rb3419@cumc.columbia.edu> https://indiaalliance.org/fellow/rakshathi-basavaraju

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Freesurfer October 2020