Freesurfer May 2014

freesurfer@nmr.mgh.harvard.edu

139 participants
206 discussions

Fwd: Welcome to the "Freesurfer" mailing list
by bara bere 21 May '14

21 May '14

im get it ---------- Forwarded message ---------- From: freesurfer-request(a)nmr.mgh.harvard.edu Date: Wed, 21 May 2014 09:51:02 -0400 Subject: Welcome to the "Freesurfer" mailing list To: bara9114(a)gmail.com Welcome to the Freesurfer(a)nmr.mgh.harvard.edu mailing list! To post to this list, send your email to: freesurfer(a)nmr.mgh.harvard.edu General information about the mailing list is at: https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer If you ever want to unsubscribe or change your options (eg, switch to or from digest mode, change your password, etc.), visit your subscription page at: https://mail.nmr.mgh.harvard.edu/mailman/options/freesurfer/bara9114%40gmai… You can also make such adjustments via email by sending a message to: Freesurfer-request(a)nmr.mgh.harvard.edu with the word `help' in the subject or body (don't include the quotes), and you will get back a message with instructions. You must know your password to change your options (including changing the password, itself) or to unsubscribe. It is: BaRa9114 Normally, Mailman will remind you of your nmr.mgh.harvard.edu mailing list passwords once every month, although you can disable this if you prefer. This reminder will also include instructions on how to unsubscribe or change your account options. There is also a button on your options page that will email your current password to you. 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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Re: [Freesurfer] Mean Thickness for each hemisphere from ?.aparc.stats
by amirhossein manzouri 21 May '14

21 May '14

Thanks Doug, I used the first link and works perfectly now! Best regards, Amirhossein Manzouri On Tue, May 20, 2014 at 5:03 PM, Douglas N Greve <greve(a)nmr.mgh.harvard.edu>wrote: > > I just ran it, and it works fine. It may be that I need to give you more > libraries. > > Start with this one > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fsutils.py > > Copy it into $FREESURFER_HOME/bin (after making a backup of the original > one) > > If that still does not work, then copy this one > > ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fsutils.pyc > > doug > > > > On 05/20/2014 04:36 AM, amirhossein manzouri wrote: > >> Dear Doug, >> Kindly find attached a sample of my lh.aparc.stats file! >> >> Best regards, >> Amirhossein Manzouri >> >> >> >> >> On Mon, May 19, 2014 at 7:59 PM, Douglas N Greve < >> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu>> wrote: >> >> Can you send me your lh.aparc.stats file? >> doug >> >> >> On 05/14/2014 01:41 PM, amirhossein manzouri wrote: >> >> >> Yes! >> >> >> On May 14, 2014 7:16 PM, "Douglas N Greve" >> <greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>>> wrote: >> >> >> Is the mean thickness in the ?h.aparc.stats file? >> Something like >> >> # Measure Cortex, MeanThickness, Mean Thickness, 2.27227, mm >> >> >> On 05/13/2014 05:18 PM, amirhossein manzouri wrote: >> >> Hi, >> The same result! the last is insula ! >> >> >> Best regards, >> Amirhossein Manzouri >> >> >> >> >> On Mon, May 12, 2014 at 5:05 PM, Douglas N Greve >> <greve(a)nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu> >> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>>>> wrote: >> >> Try this version >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/ >> greve/aparcstats2table >> >> >> >> On 05/12/2014 03:41 AM, amirhossein manzouri wrote: >> >> Hi again, >> I think I missed my question, How can I get >> the Mean >> Thickness >> of each hemisphere for several subjects using the >> aparcstats2table command? >> >> On Fri, May 9, 2014 at 4:28 PM, amirhossein >> manzouri >> <a.h.manzouri(a)gmail.com >> <mailto:a.h.manzouri@gmail.com> >> <mailto:a.h.manzouri@gmail.com >> <mailto:a.h.manzouri@gmail.com>> >> <mailto:a.h.manzouri@gmail.com <mailto:a.h.manzouri@gmail.com> >> <mailto:a.h.manzouri@gmail.com >> <mailto:a.h.manzouri@gmail.com>>> >> <mailto:a.h.manzouri@gmail.com >> <mailto:a.h.manzouri@gmail.com> >> <mailto:a.h.manzouri@gmail.com >> <mailto:a.h.manzouri@gmail.com>> >> <mailto:a.h.manzouri@gmail.com >> <mailto:a.h.manzouri@gmail.com> >> <mailto:a.h.manzouri@gmail.com >> <mailto:a.h.manzouri@gmail.com>>>>> wrote: >> >> Dear Doug, >> I have read this >> post( >> https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg25218.html >> ) >> regarding >> extracting Mean Cth of each hemisphere and >> I just get >> insula as >> the last and totally 34 numbers, I use >> aparcstats2table --hemi lh --subjects bert -m >> thickness >> --tablefile lh.Cth.bert.txt >> >> >> >> Best regards, >> Amirhossein Manzouri >> >> >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu> >> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>>> >> Phone Number: 617-724-2358 <tel:617-724-2358> >> <tel:617-724-2358 <tel:617-724-2358>> >> <tel:617-724-2358 <tel:617-724-2358> <tel:617-724-2358 >> <tel:617-724-2358>>> >> Fax: 617-726-7422 <tel:617-726-7422> >> <tel:617-726-7422 <tel:617-726-7422>> <tel:617-726-7422 >> <tel:617-726-7422> >> >> <tel:617-726-7422 <tel:617-726-7422>>> >> >> >> Bugs: >> surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting> >> <http://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> >> <http://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/ >> >> >> >> 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. >> >> >> >> -- Douglas N. Greve, Ph.D. >> MGH-NMR Center >> greve(a)nmr.mgh.harvard.edu <mailto:greve@nmr.mgh.harvard.edu> >> <mailto:greve@nmr.mgh.harvard.edu >> <mailto:greve@nmr.mgh.harvard.edu>> >> Phone Number: 617-724-2358 <tel:617-724-2358> >> <tel:617-724-2358 <tel:617-724-2358>> >> Fax: 617-726-7422 <tel:617-726-7422> <tel:617-726-7422 >> <tel:617-726-7422>> >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> <http://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> >> <http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html> >> Outgoing: >> ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ >> >> >> -- 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 <tel:617-724-2358> >> Fax: 617-726-7422 <tel: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/ >> >> >> > -- > Douglas N. Greve, Ph.D. > MGH-NMR Center > greve(a)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/ > >

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how to get scalp-cortex diff instead of white-pial diff?
by Christopher Chatham 20 May '14

20 May '14

Dear Freesurfer experts, I would like to get a map of scalp-cortex distance for every vertex on the pial surface (for use in predicting the effects of TMS). I believe there is no existing automated method for doing this. Are there any suggestions for how to calculate a scalp-cortex distance map? My current plan is simply rename my files so that the outer_skin takes the place of the pial surface, and the pial surface takes the place of the white matter boundary. Would this allow me to run mri_thickness as normal and get a scalp-cortex distance map? Alternatively, I might create a new version of mris_thickness.c in which all references to the "white" surface are replaced with references to the outer_skin surface constructed by mri_watershed, though I am new to c and thus hesitant to take this approach. (Also, I have only a MEMPRAGE and no FLASH 5/30 sequences, so I cannot use mri_make_bem_surfaces; is the latter is still considered preferable?) Any suggestions or thoughts would be highly appreciated.

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Monte Carlo Cluster Size Threshold
by Wegman, Clem J. 20 May '14

20 May '14

Hello Freesurfer Experts, I am looking for the threshold cluster size used in a Monte Carlo Simulation (ran in qdec) at p=0.05. I believe the attached pdf (used to be mc-z.abs.th13.pdf) contains this information but I am not sure about how it is annotated. Does "MaxClustBin" correspond to a cluster size (in mm^2) and "MaxClustPDF" correspond to the p-value? From this file p=0.05 would correspond to a cluster size of 375.6 mm^2. I am basing these assumptions off of a previous message from the archives (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-August/032738.ht…) although I am looking at a different file because the one suggested (cache.th13.abs.pdf.dat) did not seem to contain the correct information. Thanks a bunch for your help! -John

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freeview vs tksurfer
by S.V.Shepherd [work] 20 May '14

20 May '14

Hi all, Two questions: First, does Freeview currently support flatmaps, or -patch support still in development? Second, I notice some different behavior between tksurfer and freeview *vis-a-vis *surface overlays. In tksurfer, we were able to plot volume overlays to surfaces by specifying a registration file, e.g. * tksurfer <subjID> <hemi> inflated -overlay <funcdir>bold/<analysis>/<contrast>/<result>.nii -overlay-reg <funcdir>/bold/register.dat* though care must be taken to specify the registration, since * tksurfer <subjID> <hemi> inflated -overlay <funcdir>bold/<analysis>/<contrast>/<result>.nii* alone shows the intersection of the volume with the surface, rather than mapping the volume to the surface as desired. When I try to replicate this in freeview, by calling * freeview -f <subjdir>/surf/<hemi>.inflated:overlay=<funcdir>/bold/<analysis>/<contrast>/<result>.nii:overlay_reg=<funcdir>/bold/register.dat* I continue to get something that looks like an intersection, rather than a mapping. I can get around this by separately painting the volumes to surfaces, but if there's a way to view the data in one step, this is more desirable. Thanks! stephen *stephen v. shepherd phd* The Rockefeller University / 1230 York Avenue / New York NY 10065-6307 USA // 212.327.7620

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High Intensity Spots causing surface issues
by Jonathan Holt 20 May '14

20 May '14

Hi all, this is a recurring issue that I'm hoping I can find a solution to. Pictured is a brain with a particularly high intensity area that seems to defy surfacing. Is there a way to work around this? See attached image

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registering MRI structural data with MEG volume converted data
by Franklin Lovell Orndorff-Plunkett 20 May '14

20 May '14

Hello Freesurfer Experts, We've used the following tcsh script to convert MEG surface data, morphed to fsaverage .w paint (every timestep) format, to volume data in NIFTI format: # Convert to .nii format (volume from surface data of dSPM) placing .nii files in NII_DIR # FREESURFER_HOME is the base directory for FreeSurfer; sourcing from SetUpFreesurfer.sh setenv FREESURFER_HOME /apps/freesurfer/ && source ${FREESURFER_HOME}SetUpFreeSurfer.csh # set file numbers denoting each time step set Tmin = -0200 && set Tstep = 10 && set Tmax = 1000 # foreach FileNum (` seq -w $Tmin $Tstep $Tmax ` ) # CONVERT SURFACE DATA TO VOLUME DATA FROM PAINT TO MGZ to NII mri_surf2vol --surfval ${STC_DIR}/${SUBJECT}${STC_MORPH_SUFFIX}-30_45_80-${FileNum}.0-lh.w paint --hemi lh --volreg ${SUBJECTS_DIR}/fsaverage/mri/transforms/reg.mni152.2mm.dat --template ${SUBJECTS_DIR}/fsaverage/mri/T1.mgz --outvol ${NII_DIR}/${SUBJECT}${STC_MORPH_SUFFIX}-30_45_80-${FileNum}.0-lh.mgz mri_convert ${NII_DIR}/${SUBJECT}${STC_MORPH_SUFFIX}-30_45_80-${FileNum}.0-lh.mgz ${NII_DIR}/${SUBJECT}${STC_MORPH_SUFFIX}-30_45_80-${FileNum}.0-lh.nii mri_surf2vol --surfval ${STC_DIR}/${SUBJECT}${STC_MORPH_SUFFIX}-30_45_80-${FileNum}.0-rh.w paint --hemi rh --volreg ${SUBJECTS_DIR}/fsaverage/mri/transforms/reg.mni152.2mm.dat --template ${SUBJECTS_DIR}/fsaverage/mri/T1.mgz --outvol ${NII_DIR}/${SUBJECT}${STC_MORPH_SUFFIX}-30_45_80-${FileNum}.0-rh.mgz mri_convert ${NII_DIR}/${SUBJECT}${STC_MORPH_SUFFIX}-30_45_80-${FileNum}.0-rh.mgz ${NII_DIR}/${SUBJECT}${STC_MORPH_SUFFIX}-30_45_80-${FileNum}.0-rh.nii # mri_concat does temporal concatenation. Done this way, each image will include the left # hemisphere solution, and then the right hemisphere solution. You have to do this separately #for each hemisphere, and then add the two hemispheres together using something like #fslmaths or 3dcalc. # Have to convert mgz to nii first using e.g.: mri_convert input.mgz output.nii # e.g., 3dcalc -a left.nii -b right.nii -expr 'a+b' -prefix test_combined.nii # MERGING OF HEMISPHERES (.nii) AT EACH TIMESTEP ${AFNI_DIR}/3dcalc -a ${NII_DIR}/${SUBJECT}${STC_MORPH_SUFFIX}-30_45_80-${FileNum}.0-lh.nii -b ${NII_DIR}/${SUBJECT}${STC_MORPH_SUFFIX}-30_45_80-${FileNum}.0-rh.nii -expr 'a+b' -prefix ${NII_DIR}/${SUBJECT}${STC_MORPH_SUFFIX}-30_45_80-${FileNum}.0.nii set ExecString = 'mri_concat ' foreach FileNum (` seq -w $Tmin $Tstep $Tmax ` ) set ExecString = "${ExecString} ${NII_DIR}/${SUBJECT}${STC_MORPH_SUFFIX}-30_45_80-${FileNum}.0.nii " end The .nii files come out uniform size and a colleague suggested that I add a baseline to the original data. It seems like the issue is happening at the mri_convert step and the T1.mgz fsaverage template seems to not register properly. Is there some syntax I should be adding to the --template option in mri_surf2vol? Perhaps it's something else. -Franklin

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A newbie to fMRI analysis
by Dr Sampada Sinha 20 May '14

20 May '14

Hello I have only recently started the fmri data analysis and I downloaded freesurfer point by point from martinos site and incorporated the license file as well into the Applications/freesurfer directory. I have run into the first problem and that is of data conversion. My file is in dcm format and I have 11,000 dcm files to convert. However, before I was using Jamaan Alghamadi created gui and it is not able to convert the mri dcm files. Then I shifted to UNIX and again it is saying error. My file is on the desktop and I have given it subject id as Grace. My directory to the dcm file is '/Users/sampada/desktop/Grace. My terminal look like this before I proceed with the file conversion Last login: Mon Apr 28 15:10:13 on ttys001 dhcp020-223-179:~ sampada$ export FREESURFER_HOME=/Applications/freesurfer dhcp020-223-179:~ sampada$ source $FREESURFER_HOME/SetUpFreeSurfer.sh -------- freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0 -------- Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /Applications/freesurfer FSFAST_HOME /Applications/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /Applications/freesurfer/subjects MNI_DIR /Applications/freesurfer/mni Will anyone please let me know what I am doing wrong? I will be very grateful for any input. Thanks and regards, Sampada Senior research support specialist Molecular and neuroimaging department Department of Psychiatry 451, biomedical research building University at Buffalo (south campus) Buffalo, NY-14216

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ASL Image Exception: # 22 ERRORS
by Athanasia Monika Mowinckel 20 May '14

20 May '14

Hi. I'm trying to run an ASL analysis on my data. I have pcASL control-tag data that for the most part are getting run through the analysis without problems. However, there seems to be some difficulties with the calibration. I'm running the command as root in csh: oxford_asl -i $INPUT/analysis/diffdata -o $INPUT/analysis/KMI_data --tis 3.6 --bolus 1.8 --bat 1.8 --casl \ --t1b 1.6 --alpha 0.98 --artoff --fixbolus \ --infert1 -s $ANATFOLDER/anat_roi_brain --report \ --regfrom $INPUT/PCASLmean_brain --spatial \ -c $INPUT/M0.nii.gz --tr 12 the error is such: Number of voxels is:81920 Number of repeats in data is:70 Outputting ASL data mean at each TI Done. OXFORD_ASL - running Creating output directory Saving results in natve (ASL aquisition) space to ASL/analysis/KMI_data/native_space Saving results in structural space to ASL/analysis/KMI_data/struct_space Pre-processing Creating mask Performing registration ASL_REG Input file is: /ASL/PCASLmean_brain Running FLIRT Tidying up ASL_REG - Done. Segmenting the structural image Calculating M0a - calling ASL_CALIB ASL_CALIB Tissue reference is: csf *Image Exception : #22 :: ERROR: Could not open image /tmp/fsl_SsEGkZ_asl_calib/seg_bias* *libc++abi.dylib: terminating with uncaught exception of type RBD_COMMON::BaseException* */usr/local/fsl/bin/asl_calib: line 568: 58142 Abort trap: 6 ${FSLDIR}/bin/applywarp --ref=$calib --in=$temp_calib/seg_bias --out=$temp_calib/biasfield --premat=$temp_calib/high2low.mat --super --interp=spline --superlevel=4* *Cannot open volume /tmp/fsl_SsEGkZ_asl_calib/biasfield for reading!* *Image Exception : #22 :: ERROR: Could not open image /tmp/fsl_SsEGkZ_asl_calib/sens* *libc++abi.dylib: terminating with uncaught exception of type RBD_COMMON::BaseException* */usr/local/fsl/bin/asl_calib: line 689: 58150 Abort trap: 6 fslmaths $temp_calib/calib -div $temp_calib/sens $temp_calib/calib* M0:874.58000000000000000000 ASL_calib - DONE. Best regards, Athanasia Mowinckel

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mris_anatomical_stats lgi error
by _andreia_＠sapo.pt 20 May '14

20 May '14

Hello all, I generated the lgi.stats file for all my subjects and in one of them I got this warning: mris_anatomical_stats -a aparc.annot -t pial_lgi -f SUBJ/stats/lh.aparc_lgi.stats SUBJ lh computing statistics for each annotation in aparc.annot. using thickness file pial_lgi. reading volume /home/user/visao/Freesurfer//SUBJ/mri/wm.mgz... reading input surface /home/user/visao/Freesurfer//SUBJ/surf/lh.white... reading input pial surface /home/user/visao/Freesurfer//SUBJ/surf/lh.pial... reading input white surface /home/user/visao/Freesurfer//SUBJ/surf/lh.white... MRISREADANNOTATIONINTOARRAY: VERTEX INDEX OUT OF RANGE: 150843 I=007D324B, IN_ARRAY_SIZE=150843 ANNOT FILE: /HOME/USER/VISAO/FREESURFER//SUBJ/SURF/../LABEL/LH.APARC.ANNOT MRISreadAnnotationIntoArray: vertex index out of range: 150844 i=007D324B, in_array_size=150843 annot file: /home/user/visao/Freesurfer//SUBJ/surf/../label/lh.aparc.annot MRISreadAnnotationIntoArray: vertex index out of range: 150845 i=007D324B, in_array_size=150843 annot file: /home/user/visao/Freesurfer//SUBJ/surf/../label/lh.aparc.annot (...) reading colortable from annotation file... colortable with 36 entries read (originally /autofs/space/terrier_001/users/nicks/freesurfer/average/colortable_desikan_killiany.txt) structure is "bankssts" number of vertices = 1139 total surface area = 795 mm^2 total gray matter volume = 2868 mm^3 average cortical thickness = 3.820 mm +- 0.158 mm average integrated rectified mean curvature = 0.117 average integrated rectified Gaussian curvature = 0.031 folding index = 10 intrinsic curvature index = 1.3 structure is "caudalanteriorcingulate" number of vertices = 812 (...) Even thought there was the warning, everything seems to be fine with the lgi values, should I be concerned about this or I may just ignore it? Thank you! Andreia

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Freesurfer May 2014