Freesurfer

freesurfer@nmr.mgh.harvard.edu

15 participants
30097 discussions

hippocampal subfields question
by Salil Soman 12 Aug '13

12 Aug '13

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

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funcroi-table-sess error
by Alexandra Tanner 12 Aug '13

12 Aug '13

Dear Doug and Freesurfers, I am attempting to run funcroi-table-sess on a set of subjects but keep getting an error message I've never seen before: funcroi-table-sess -roi /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/ctx.lh.insula.aparc+aseg_2vFix.roicfg -sf /cluster/roffman/users/Stable5_PerRun/Subject_Files/30_ActiveFolateAndPlacebo_PostPrePAIRED -c Cond2vFix -o /cluster/roffman/users/Stable5_PerRun/ROI_Analysis/FB12/18ActiveFolate_12Placebo_PreAndPost_7Tpost/ctx_lh_insula_aparc+aseg_2vFix log/funcroi-table-sess.log log/funcroi-table-sess.log: No such file or directory. Funcroi-sess ran without error, as did funcroi-config. I've run this analysis many times in the past and have never had this problem so I am at a loss as to what is going wrong. Any help would be greatly appreciated! Thanks, Alex

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recon-all after manual edits
by Jason Tourville 12 Aug '13

12 Aug '13

Hi there, I am doing manual edits on the brainmask.mgz, wm.mgz, and brain.finalsurfs.manedit.mgz volumes and adding control points. What autorecon flag or from which stage of processing should I rerun recon-all such that all of these manual edits are respected? Thanks, Jason -- Jason A. Tourville, Ph.D. Research Assistant Professor Department of Speech, Language, and Hearing Sciences Boston University 677 Beacon St. Boston, MA 02215 Phone: (617)353-9484 Fax: (617)353-7755

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Re: [Freesurfer] Error when using preproc-sess -per-session in FS-5.3
by Sepide Movaghati 12 Aug '13

12 Aug '13

Just an update! FS 5.3 gives me the same error even when running -per-run. Using FS 5.1, the same error pops up only in -per-session and -per-run works fine. Thank you in advance. ________________________________ From: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu] on behalf of Sepide Movaghati [sepide.movaghati(a)mail.mcgill.ca] Sent: Monday, August 12, 2013 11:31 AM To: freesurfer(a)nmr.mgh.harvard.edu Subject: [Freesurfer] Error when using preproc-sess -per-session in FS-5.3 Hello, I am using freesurfer 5.3 and try to run: preproc-sess -s session1 -surface self lhrh -fsd bold -mni305 -fwhm 5 -per-session it gives me an error: 1/1 session1 1/1 session1 003 lh --------- Mon Aug 12 11:21:09 EDT 2013 ERROR: could not determine file for /export01/data/sepid/subjects/ZY/session1/bold/003/fmcpr however, it works fine when I use -per-run. I have attached complete terminal output. Thanks.

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FreeSurfer version for subjects
by Alex Hanganu 12 Aug '13

12 Aug '13

Hello everyone, isthere a method to verify which was the last version of FreeSurfer that was used to perform the recon-all ? For. ex. in /subjects/subject_name/scripts/build-stamp.txt/I can see that this subject was registered the first time with FS version 5.0but after that, an additional recon-all was performed and all the pre-processing steps have been passed with FS version 5.3, and this is registered in /recon-all-status.log/. Yet, in this log the version of FS that was used - is not shown. Thanks, Alex.

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jittered ITI and null trials
by Lukito, Steve 12 Aug '13

12 Aug '13

Hi there, Please ignore my earlier question. The Cygwin is still a mystery to me but I have managed to run the optseq2 on a UNIX computer. It seems there is no way to input jittered ITI and null trials at the same time in optseq2, is this right? This is because null trials by definition is equal to jitter (this is how I understand Douglas Greve's slides). Unfortunately, I would like to replicate an experiment with three experimental conditions with four types of trials (=the exp conditions plus null trials). Each trial is jittered so that its length is between 2850 and 3350 ms long, which include the 1000 ms stimulus presentation. My thought is to use psdwin=0 - 1850 ms (2850 ms minus 1000 ms stim presentation) for now and then later on replace this constant time window with the jittered ones (randomized). I assume that if I can build an optimum sequence for the shorter boundary of the ITI, they will still be as optimum when I replace the post-stimulus time window with the jittered one provided that the jittered time interval is of longer span. I am not sure if this is even remotely true so I would really appreciate anyone's comment on this. Best, Steve

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editing topological defect
by pietro de rossi 12 Aug '13

12 Aug '13

Hi freesurfers, I have a problem editing a topological defect given that it is represented by cortex non included within the pial boundary without white matter in it. The problem is I can't use white matter to place control points and/or edit voxel in the aux wm.mgz volume... I'm attaching an image... the area I'm talking about is indicated by green arrows. Thanks in advance, Pietro -- Pietro De Rossi, MD ------------------------------------- Sapienza Università di Roma, Facoltà di Medicina e Psicologia, Dipartimento NESMOS (Neuroscienze, Salute Mentale, Organi di Senso), Ospedale Sant'Andrea, Via di Grottarossa 1035-1039, 00189 Roma NESMOS Department (Neurosciences, Mental Health and Sensory Functions), School of Medicine and Psychology, Sapienza University, Sant’Andrea Hospital, Via di Grottarossa 1035-1039, 00189 Rome, Italy Neurobehavioral Clinical Research Section, Social and Behavioral Research Branch, National Human Genome Research Institute (NHGRI), National Institutes of Health (NIH), Bethesda, Maryland 20892, USA

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Validation of results
by Sinead Kelly 12 Aug '13

12 Aug '13

Dear freesurfer users, I would really appreciate if anybody could confirm that I have preformed my analysis correctly as I have very little experience with freesurfer and I want to make sure that my result is a true finding. Firstly, I am looking at the effect of a schizophrenia risk variant on cortical surface area in a large sample of healthy controls. a. I performed preprocessing on all of my subjects using *recon-all.* b. I then qcached my data (resampling it to the average subject -* fsaverage *) c. An FSGD file was then created for statistical analysis to look at differences between TT carriers and TG carriers with age and gender as covariates of no interest. Here is an example of the file I created: GroupDescriptorFile 1 Title MIR137 Class TTMale Class TTFemale Class TGMale Class TGFemale Variables Age Input CON3140 TGFemale 37 Input CON3891 TTFemale 33 Input CON4664 TTFemale 40 Input CON5591 TTMale 41 Input CON7009 TGMale 21 Input CON7024 TTMale 59 Input CON7038 TTMale 56 Input CON7050 TTMale 30 Input CON7054 TTMale 43 Input CON7055 TTMale 43 Input CON7072 TTFemale 41 d. I applied the following contrast: -0.5 -0.5 0.5 0.5 0 0 0 0 e. I followed the online tutorial by firstly running the *mris_preproc*script with *area.fwhm10.fsaverage* as my input file. Is this correct? (I ran this separately for the left and right hemisphere). f. I then ran the *mri_glmfi*t script followed by the *mri_glmfit-sim*script: *mri_glmfit-sim --glmdir rh.MIR137_area.glmdir --sim mc-z 5000 1.3 mc-z.abs --sim-sign abs --cwpvalthresh .999 --overwrite* (I ran this separately for each hemisphere) Does this look correct? When this ran I then checked the *mc-z.abs.sig.cluster.summary file:* ClusterNo Max VtxMax Size(mm^2) MNIX MNIY MNIZ CWP CWPLow CWPHi NVtxs Annot 1 -3.298 36614 541.01 -26.0 -53.1 62.2 0.77340 0.76580 0.78100 1177 superiorparietal 2 2.918 9004 1642.43 -8.5 9.7 65.2 *0.01020* 0.00840 0.01200 2790 superiorfrontal 3 2.626 126211 363.55 -30.3 -65.2 40.5 0.98580 0.98360 0.98800 817 inferiorparietal 4 2.441 6490 313.02 -30.5 -35.1 58.4 0.99660 0.99560 0.99760 693 postcentral 5 2.375 107140 1095.56 -10.9 -57.2 44.7 0.09720 0.09180 0.10260 2308 precuneus 6 2.347 132687 414.79 -38.6 2.1 24.8 0.95300 0.94920 0.95680 974 precentral 7 2.284 97632 1510.86 -41.4 -50.0 -14.4 *0.01820* 0.01580 0.02060 2446 fusiform 8 2.122 111909 365.94 -49.2 -29.5 -3.0 0.98480 0.98260 0.98700 837 superiortemporal 9 2.070 74111 444.95 -54.7 -42.0 6.3 0.92120 0.91620 0.92600 998 bankssts 10 1.809 85712 281.07 -57.0 -30.8 21.7 0.99860 0.99800 0.99920 598 supramarginal 11 1.796 121724 312.87 -10.0 64.3 6.5 0.99660 0.99560 0.99760 485 superiorfrontal I have two significant results here - does this look okay? Does this result indicate that surface area of the fusiform and superior frontal significantly differ between TT and TG carriers (corrected for multiple comparisons?). How can I check or report the statistics? Is it possible to extract the values and report descriptive as well as inferential statistics for the result? I would really appreciate if anyone can validate this for me as I have very little experience with freesurfer. Thank you for your help! Sinead Sinead Kelly Neuropsychiatric Genetics Group Trinity Centre St. James's Hospital Dublin 8

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Re: [Freesurfer] mean thickness over hemisphere in stats file
by Bruce Fischl 12 Aug '13

12 Aug '13

Hi Ines sorry, this was my mistake. The command is "mris_anatomical_stats" NOT "mris_anatomical_thickness". If your SUBJECTS_DIR is set properly, you can run: mris_anatomical_stats -l $SUBJECTS_DIR/$subject/label/$hemi.cortex \ $subject $hemi where $hemi is lh or rh and $subject is the subject id you want to quantify cheers Bruce On Mon, 12 Aug 2013, Mürner-Lavanchy, Ines wrote: > ________________________________________ > From: Bruce Fischl [fischl(a)nmr.mgh.harvard.edu] > Sent: Friday, 9 August 2013 3:36 PM > To: Mürner-Lavanchy, Ines > Cc: freesurfer(a)nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] mean thickness over hemisphere in stats file > > Hi Ines > > I think mris_anatomical_thickness is your best bet. You probably want to > specify the ?h.cortex.label file with the -l flag so that it ignores > non-cortical regions > > cheers > Bruce > > > On Fri, 9 Aug 2013, Mürner-Lavanchy, Ines wrote: > >> Dear experts, >> >> please excuse my question, I'm a beginner. I really searched for an answer >> in the archive, but I couldn't find out what I was doing wrong. >> >> I would like to write the mean cortical thickness of a hemisphere in the >> stats file. I read one can do that by using -m thickness. >> Where in the command line do I have to put it? I tried various versions, but >> it doesn't work. >> >> This would be the command: >> >> aparcstats2table --hemi rh --parc aparc --meas thickness --tablefile >> "directory"//"filename" --m thickness --subjects 1 2 3 4 >> SUBJECTS_DIR : "directory" >> >> Where do I include the -m thickness option? Or do I have to add something >> else? >> >> Thank you very much for your help, >> Ines >> >> > > > 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. > > >

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Optseq2 with Cygwin
by Lukito, Steve 12 Aug '13

12 Aug '13

Dear optseq2 developers, I would like to use optseq2 to develop optimal sequence for my MRI experiment. I have a windows machine (Windows 7, SP1, 64-bit OS) so I installed Cygwin-64 to run the optseq2. What I've done so far: - Downloaded optseq2.exe (Cygwin version) and put this into the Cygwin-64 folder - I run Cygwin and change my directory to Cygwin-64 where the optseq2 is - I followed instructions from previous email trails so I typed in chmod a+x optseq2 (to make optseq2 executable within the shell?) - Then I typed in ./optseq2 (since typing in optseq2 on its own results in -bash: optseq2: command not found) On both occasions (chmod... and ./optseq2), the command prompt returns without output. As I understand it, at least, for the second command I should get the help text for optseq? Have I done something wrong? Would really appreciate you help! Steve PS I am not familiar with UNIX so please be patient if my question is trivial :). Steve Lukito, MSc. PhD Candidate | Institute of Psychiatry | King's College London Department of Child and Adolescent Psychiatry - PO85 16 De Crespigny Park London SE5 8AF Phone: 0207 848 0469

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