Freesurfer July 2016

freesurfer@nmr.mgh.harvard.edu

143 participants
252 discussions

fornix segmentation using recon-all
by Hari Guragain 10 Jul '16

10 Jul '16

Dear Freesurfer Experts, I am interested to get the volume information of the structure "fornix" in the aseg.stats file. I would appreciate if there is any such argument that can be used along with the recon-all to get the volume information of the fornix like below. Till now, I have been using · *recon-all -autorecon-all -subjid **your_subject_name* Any suggestions will be appreciated. # ColHeaders Index SegId NVoxels Volume_mm3 StructName normMean normStdDev normMin normMax normRange 1 4 6489 6958.2 Left-Lateral-Ventricle 34.8514 11.5767 15.0000 82.0000 67.0000 Thank you, Hari Guragain

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Question about write_surf.m
by Dulce Maria Magdaleno Arroyo 10 Jul '16

10 Jul '16

Hi freesurfers! I'm trying to run the function write_surf in matlab, as far as I understand this function is to write a surface to analyze in freesurfer from matlab data. I'm not sure if the extension of the file name has to be different, so I need your help to solve this simple (I guess) problem. The first line is what I'm trying to run and the next lines show me the error. *write_surf('prueba.nofix/', vertices, faces);* *...subtracting 1 from face indices for FreeSurfer compatibility*. *Error using fwriteInvalid file identifier. Use fopen to generate a valid file identifier.Error in fwrite3 (line 29)fwrite(fid, b1, 'uchar') ;Error in write_surf (line 38)fwrite3(fid, TRIANGLE_FILE_MAGIC_NUMBER);* thank you in advance for your help! Dulce

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Surface segmentation for resting state
by ERIK JAHNER 09 Jul '16

09 Jul '16

Dear free surfer experts, I am conducting a resting state fMRI study using a lagged analysis method. To do this method on a volume, I have used 6 mm cubes as rois covering the whole brain but masked for grey matter. I use these values in a correlation map. I would like to do a similar approach here. Is there a way to get measurements ~6mm apart averaging the vertices 3 mm away. basically, I would like to parcel the cortex surface map into 6mm rois evenly distributed over the surface of the cortex. I would like to take advantage of the fact that I can take measurements along surfaces and not across sulci. Is there an automated way or easy way of building this ROI map. Erik Jahner

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Re: FSFAST error: ERROR: fast_selxavg3() failed\n matlab command not found
by ERIK JAHNER 09 Jul '16

09 Jul '16

On Jul 09, 2016, at 09:00 AM, freesurfer-request(a)nmr.mgh.harvard.edu wrote: Send Freesurfer mailing list submissions to freesurfer(a)nmr.mgh.harvard.edu To subscribe or unsubscribe via the World Wide Web, visit https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer 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. Longitudinal LME contrast vectors (K) 2. Re: Longitudinal LME contrast vectors (Martin Reuter) 3. Question about NULL event with Optseq2 (Feng Zhou) 4. Cerebral volume without ventricles (Kaiming Yin) 5. Re: FSFAST error: ERROR: fast_selxavg3() failed\n (Douglas Greve) ---------------------------------------------------------------------- Message: 1 Date: Fri, 8 Jul 2016 15:02:58 -0700 From: K <kam.ntnu(a)gmail.com> Subject: [Freesurfer] Longitudinal LME contrast vectors To: freesurfer(a)nmr.mgh.harvard.edu Message-ID: <CAH54DzgqKWSCwm0gu_ecbB3jrQmLc=Y6Nun5j4DujKwaxn78UA(a)mail.gmail.com> Content-Type: text/plain; charset="utf-8" Hello! We are trying to run a longitudinal morphometry analysis with a control group and clinical group scanned twice. We'd like to look at group x time interactions and would like help figuring out the best way to do so. As the time variable we use centered age -- the deviation from the mean age across all subjects and timepoints. To do so, we use the following lme model: intercept + centeredage.controls + centeredage.clinical + group(0,1) + sex(0,1) Contrast vector: [0 1 -1 0 0] where the centeredage column contains only the centered age for that group and zeros for the opposite group. The thinking behind this is to investigate which cortical regions show opposite effects of time between the groups. However, the FreeSurfer lme software requests a specified "time column". Obviously, we cannot add a centered age for all subjects, nor does it seem to make sense to use one of the two group-specific centeredage columns as the time column. Our alternative model for investigating interatction is: intercept + centeredage + group(0,1) + sex(0,1) + groupxcenteredage where centeredage is the time columns and is a common regressor for both groups and thus, groupxcenteredage becomes 0 for control subjects. Contrast vector: [0 0 0 0 1] This would test whether there is an added effect of centered age in the clinical group. Is there a better way to do an group x time interaction analysis here, or is there a solution for the time column? Thanks!

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Re: [Freesurfer] FSFAST error: ERROR: fast_selxavg3() failed\n
by Douglas Greve 09 Jul '16

09 Jul '16

what do you mean nothing happens? After you hit the return key, it should either give you the path to the command or it should say Command not found. doug ps. Please remember to post to the list and not to us individually On 7/8/16 7:16 PM, Erik Jahner wrote: > When I type "which matlab” in the command window, nothing happens. My > $PATH structure is a s follows: > > echo $PATH > /Applications/freesurfer/bin:/Applications/freesurfer/fsfast/bin:/Applications/freesurfer/tktools:/usr/local/fsl/bin:/Applications/freesurfer/mni/bin:/opt/local/bin:/opt/local/sbin:/opt/local/bin:/opt/local/sbin:/usr/local/bin:/usr/bin:/bin:/usr/sbin:/sbin:/opt/X11/bin > > Sorry if my response seems naïve, I’am new to running command > lines although I’m trying learn. > > Erik > > Message: 6 > Date: Fri, 8 Jul 2016 14:30:43 -0400 > From: Douglas N Greve <greve(a)nmr.mgh.harvard.edu > <mailto:greve@nmr.mgh.harvard.edu>> > Subject: Re: [Freesurfer] FSFAST error: ERROR: fast_selxavg3() > failed\n > To: freesurfer(a)nmr.mgh.harvard.edu <mailto:freesurfer@nmr.mgh.harvard.edu> > Message-ID: <577FF153.1080602(a)nmr.mgh.harvard.edu > <mailto:577FF153.1080602@nmr.mgh.harvard.edu>> > Content-Type: text/plain; charset=windows-1252; format=flowed > > Is matlab in your path? What happens if you type > which matlab > at the command line? > > On 07/08/2016 12:34 AM, ERIK JAHNER wrote: >> >> Hello FreeSurfer Developers, >> >> >> This is Erik Jahner, I?m attempting to complete the final step in the >> tutorial concerning FSFast Functional connectivity walkthrough >> (http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkth… ), >> >> but for I get the following error when I run the following command: >> >> selxavg3-sess -s subj439rest -a fc.lpccseed.surf.lh >> >> >> Mon Jul 4 11:01:41 PDT 2016 >> >> rawfunc2surf-sess completed >> >> ---------------------------------------- >> >> Started at Mon Jul 4 11:01:40 PDT 2016 >> >> Ended at Mon Jul 4 11:01:41 PDT 2016 >> >> preproc-sess done >> >> ------------------------------------------- >> >> /Applications/freesurfer/LagStructure/subj439rest >> >> Mon Jul 4 11:01:41 PDT 2016 >> >> anadir = >> /Applications/freesurfer/LagStructure/subj439rest/rest/fc.lpccseed.surf.lh >> >> DoGLMFit = 1 >> >> DoContrasts = 1 >> >> UpdateNeeded = 1 >> >> ------------------------------------------ >> >> ------- matlab output -------------------- >> >> matlab: Command not found. >> >> ------------------------------------------ >> >> *ERROR: fast_selxavg3() failed\n* >> >> >> I've searched the list and no similar errors have been reported. I >> have tried to reinstall MATLAB; I have tried following the >> instructions to install the runtime environment; I have tried redoing >> all analysis from scratch. I have noticed that STEP 5 does not work >> unless I change the -cfg from ?L_Posteriorcingulate.config? >> to ?mean.L_Posteriorcingulate.config?. I don?t think this is the >> problem, but I thought I would point it out. >> >> My session directory is ?subj439rest? >> >> Instead of titling the sub directory ?bold?, I titled it ?rest? >> >> >> 1) FreeSurfer version: freesurfer-Darwin-lion-stable-pub-v5.3.0 >> >> 2) Platform: OSX Yousemite >> >> 3) uname -a: Darwin ERIKs-iMac.local 15.5.0 Darwin Kernel Version >> 15.5.0: Tue Apr 19 18:36:36 PDT 2016; >> root:xnu-3248.50.21~8/RELEASE_X86_64 x86_64 >> >> 4) selxavg3-sess-rest-fc.lpccseed.surf.lh-160704110140.log: see attached >> >> ___________________________________________________ >> >> Here are the command lines I put in for steps 4-8, incase this is of >> some use: >> >> STEP 4 >> >> fcseed-config-segid 1010 -fcname L_Posteriorcingulate.dat -fsd rest >> -mean-cfg mean.L_Posteriorcingulate.config >> >> STEP 5 >> >> fcseed-sess-s subj439rest -cfg mean.L_Posteriorcingulate.config >> >> STEP 6 >> >> * fcseed-config -wm -fcname wm.dat -fsd rest -pca -cfg wm.config >> * fcseed-sess -s subj439rest -cfg wm.config >> >> * fcseed-config -vcsf -fcname vcsf.dat -fsd rest -pca -cfg vcsf.config >> * fcseed-sess -s subj439rest -cfg vcsf.config >> >> STEP7 >> >> mkanalysis-sess-analysis fc.lpccseed.surf.lh -surface fsaverage lh >> -fwhm 5 -notask-taskreg L_Posteriorcingulate.dat 1 -nuisreg vcsf.dat 5 >> -nuisreg wm.dat 5 -mcextreg-polyfit 5 -nskip 4 -fsd rest -TR 2 -per-run >> >> STEP 8 >> >> selxavg3-sess-s subj439rest -a fc.lpccseed.surf.lh >> >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu <mailto:Freesurfer@nmr.mgh.harvard.edu> >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)nmr.mgh.harvard.edu <mailto:greve@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 > 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/ > > > > ------------------------------

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Cerebral volume without ventricles
by Kaiming Yin 09 Jul '16

09 Jul '16

Dear FS experts, Could I ask which value in the aseg.stats file represent the whole cerebral volume without ventricles? Thanks, Kaiming

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Longitudinal LME contrast vectors
by K 08 Jul '16

08 Jul '16

Hello! We are trying to run a longitudinal morphometry analysis with a control group and clinical group scanned twice. We'd like to look at group x time interactions and would like help figuring out the best way to do so. As the time variable we use centered age -- the deviation from the mean age across all subjects and timepoints. To do so, we use the following lme model: intercept + centeredage.controls + centeredage.clinical + group(0,1) + sex(0,1) Contrast vector: [0 1 -1 0 0] where the centeredage column contains only the centered age for that group and zeros for the opposite group. The thinking behind this is to investigate which cortical regions show opposite effects of time between the groups. However, the FreeSurfer lme software requests a specified "time column". Obviously, we cannot add a centered age for all subjects, nor does it seem to make sense to use one of the two group-specific centeredage columns as the time column. Our alternative model for investigating interatction is: intercept + centeredage + group(0,1) + sex(0,1) + groupxcenteredage where centeredage is the time columns and is a common regressor for both groups and thus, groupxcenteredage becomes 0 for control subjects. Contrast vector: [0 0 0 0 1] This would test whether there is an added effect of centered age in the clinical group. Is there a better way to do an group x time interaction analysis here, or is there a solution for the time column? Thanks!

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Segmentation of hippocampal subfields with current dev version
by Eric A Nelson 08 Jul '16

08 Jul '16

Hello, I am trying to use the hippocampal subfield segmentation presented in the Iglesias paper. I downloaded and installed the latest available dev version about a week ago, along with FSL and the Matlab 2012b runtime. I attempted to run the pipeline and the hippocampal subfield segmentation together. The primary pipeline ran successfully as indicated by the log as well as manually checking the output in freeview. The hippocampal subfield segmentation did not complete successfully and the subsequent output files are nowhere to be found. I checked the archive and saw that someone had a similar issue back in October. Based on the archive I have done the following trouble shooting steps: 1) I made sure that /Applications/freesurfer/MCRv80/bin/maci64/libmwi18n.dylib does exist. 2) I also tried unsetting the DYLD_LIBRARY_PATH as followed: In bash: unset DYLD_LIBRARY_PATH In (t)csh: unsetenv DYLD_LIBRARY_PATH Then I reran the hippocampal segmentation as follows: recon-all -s [subject] -hippocampal-subfields-T1 Still no success and not sure what else I can do. I am including both the recon-all.log and hippocoampal-subfields-T1.log. Best, Eric Nelson Neuroimaging and Translational Research Lab UAB

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Refining subcortical structures
by Dorsa Haji Ghaffari 08 Jul '16

08 Jul '16

Hi, I want to refine the surface of my segmented subcortical structures such as thalamus. I know -fix is used for refining the cortex surface, but is there any function that refines the subcortical structures? Thank you Dorsa

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qdec error
by shi yao wang 08 Jul '16

08 Jul '16

Dear FS experts: I am trying to qdec to analysis FS results. when I loading qdec.table.dat, it shows cannot open the data (could not fine column name of fsid or ID) Following is my qdec files: /home/Lawrence/Lawrence_data fsid Gender age diagnosis L_frontal_V L_cingulate_V L_occipital_V L_temporal_V L_parietal_V L_insula_V R_frontal_V R_cingulate_V R_occipital_V R_temporal_V R_parietal_V R_insula_V 201 male 26 RT 90473 12084 21898 59241 62664 5899 85844 11010 19002 56413 60214 6085 202 male 21 RT 97466 10844 25305 59970 60806 7282 96692 12076 26222 61450 61593 7172 203 female 27 RT 72102 10805 17281 47113 47328 5990 72102 10805 17281 47113 47328 5990 301 female 19 Control 71977 7757 17074 44763 45861 5627 68432 8775 17099 44247 48478 5407 302 female 21 Control 81139 11166 23599 56458 51749 6361 80712 9279 24278 54830 54307 6596 303 male 20 Control 99284 11845 26018 65006 60851 7058 96242 10520 23110 61714 67203 7235 error message: Loading data table /home/Lawrence/Lawrence_data/qdec/qdec.table.dat... ERROR: QdecDataTable::Load could not find column named 'fsid' or 'ID' in /home/Lawrence/Lawrence_data/qdec/qdec.table.dat! Error loading the data table. Thanks Lawrence

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Freesurfer July 2016