Freesurfer

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30132 discussions

Re: [Freesurfer] tracula -bedp - path
by Anastasia Yendiki 26 Jul '12

26 Jul '12

Hi Keith - This seems to be a different problem here, since all the bedpostx outputs are there and are loaded in without a problem. The error occurs after that. What's the size of your images? Does the mask file look normal? Thanks, a.y On Thu, 26 Jul 2012, Keith Yoder wrote: > Hi, > > Was there any resolution to this issue? I'm having a similar problem > running trac-all on a Linux cluster. > > I think bedpostx works if I call it directly from the command line twice. > The first time, bedpostx_postproc.sh doesn't seem to work and the > *samples.nii.gz files are only created if I rerun bedpostx. However, > trac-all...-path fails. I've attached the trac-all-path output and pasted > the relevant section below: > > Creating output directory/mnt/ide0/home/kjyoder/research/conduct_disorder/fs/1001/dpath/lh.cst_AS_av > g33_mni_flt > Loading DWIs from > /mnt/ide0/home/kjyoder/research/conduct_disorder/fs/1001/dmri/dwi.nii.gz > Loading mask from/mnt/ide0/home/kjyoder/research/conduct_disorder/fs/1001/dlabel/diff/aparc+ > aseg_mask.flt.nii.gz > Loading BEDPOST parameter samples from > /mnt/ide0/home/kjyoder/research/conduct_disorder/fs/1001/dmri.bedpostX > Loading segmentation map from/mnt/ide0/home/kjyoder/research/conduct_disorder/fs/1001/dlabel/mni/aparc+a > seg.nii.gz > Loading b-values from > /mnt/ide0/home/kjyoder/research/conduct_disorder/fs/1001/dmri/bvals > Loading gradients from > /mnt/ide0/home/kjyoder/research/conduct_disorder/fs/1001/dmri/bvecs > Segmentation fault (core dumped) > > Here are the contents of the subjects bedpostX directory: > > bvals > bvecs > commands.txt > diff_slices > dyads1_dispersion.nii.gz > dyads1.nii.gz > dyads2_dispersion.nii.gz > dyads2.nii.gz > logs > mean_dsamples.nii.gz > mean_f1samples.nii.gz > mean_f2samples.nii.gz > mean_ph1samples.nii.gz > mean_ph2samples.nii.gz > mean_S0samples.nii.gz > mean_th1samples.nii.gz > mean_th2samples.nii.gz > merged_f1samples.nii.gz > merged_f2samples.nii.gz > merged_ph1samples.nii.gz > merged_ph2samples.nii.gz > merged_th1samples.nii.gz > merged_th2samples.nii.gz > monitor > nodif_brain_mask.nii.gz > xfms > > Also, I'm attaching the bvals, bvecs, dmrirc.local, trac-all.error, and > trac-all.log for the subject. Let me know if there is any other information > you need. > > Thanks in advance, > Keith > -- > Keith YoderPhD Candidate, Integrative Neuroscience > Social Cognitive Neuroscience Laboratory > The University of Chicago > 5846 S. University Avenue, Kelly 312 > Chicago, IL 60637 > Phone: 574-215-9678 > kjyoder(a)uchicago.edu > > > > > On Fri, Oct 7, 2011 at 10:04 AM, Anastasia Yendiki > <ayendiki(a)nmr.mgh.harvard.edu> wrote: > > Hi Judit, > > 1. If you can run bedpostx directly then you should do: > bedpostx /usr/local/freesurfer/subjects/C001/dmri > > Note that this dmri directory and the one you tried to run > bedpostx_single_slice.sh on are different, so I'm not sure which > location is the right one where your data is, but in any case > you don't need to run bedpostx_single_slice.sh. > > 2. The error seems to occur either when it's reading the bvecs > file, or right after that when it's accessing the bedpostx > outputs. So I'd try to look those for that subject and see if > everything is ok. > > Hope this helps, > a.y > > On Fri, 7 Oct 2011, Judit Haasz wrote: > > > Hi, > > I ran into 2 problems related to tracula. > > 1. trac-all -bedp command exits with following > message. > > WARN: Running FSL's bedbost locally - this might > take a while > >> > WARN: It is recommended to run this step on a > cluster > >> > bedpostx_seychelles > /usr/local/freesurfer/subjects/C001/dmri > >> > subjectdir is > /usr/local/freesurfer/subjects/C001/dmri > >> > Making bedpostx directory structure > >> > Queuing preprocessing stages > >> > [: 223: NONE: unexpected operator > >> > [: 314: NONE: unexpected operator > >> > [: 327: xbedpostx_pre: unexpected operator > >> > [: 486: x: unexpected operator > >> > [: 486: -le: argument expected > >> > Queuing parallel processing stage > >> > [: 223: NONE: unexpected operator > >> > [: 327: xbedpostx: unexpected operator > >> > [: 486: x53: unexpected operator > >> > 0 slices processed > >> > Queuing post processing stage > >> > [: 223: NONE: unexpected operator > >> > [: 314: NONE: unexpected operator > >> > [: 327: xbedpostx_post: unexpected operator > >> > [: 486: x: unexpected operator > >> > [: 486: -le: argument expected > >> > > > This problem has been posted in May and June. > bedpostx from command line > runs perfectly and that is how I have been running > it so far. One of u > suggested to try the following: > > /usr/local/fsl/bin/bedpostx_single_slice.sh/disks/open/judit/subjects/diffu > sion_tutorial/dtisubjects2005/subj_523/dmri > 2 1 1000 1250 25 1 0 > > then I got: > > ** ERROR (nifti_image_read): failed to find header > filefor'/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/ > dmr > i/data_slice_0000' > **ERROR:nifti_image_open(/disks/open/judit/subjects/diffusion_tutorial/dtisub > jects2 > 005/subj_523/dmri/data_slice_0000): bad header info > ERROR: failed to openfile/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523/ > dmri > /data_slice_0000 > ERROR: Could not openimage/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_523 > /dmri > /data_slice_0000 > Image Exception : #22 :: Failed to readvolume/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_52 > 3/dmri > /data_slice_0000 > > An exception has been thrown > Failed to readvolume/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_52 > 3/dmri > /data_slice_0000Trace: read_volume4DROI. > > Done > > Can u suggest a reason behind all this? This happens > on Linux machine > (2.6.35-28-generic #50-Ubuntu 10.10, x86_64, Java VM > Version: Java > 1.6.0_17-b04 with Sun Microsystems Inc. Java > HotSpot(TM) 64-Bit Server VM > mixed mode). > On Mac OS X (version 10.7.1 - Lion, 2 x 2.66 GHz > 6-core Intel Xeon > processors, 32 GB 1333 MHz DDR3 RAM) trac-all -bedp > runs well. > > My other question is: > trac-all -path exists with error (in case of a > single subject): > > Loading DWIsfrom/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/ > dmri > /dwi.nii.gz > Loading maskfrom/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/ > dlab > el/diff/aparc+aseg_mask.bbr.nii.gz > Loading BEDPOST parameter samplesfrom/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/ > dmri > .bedpostX > Loading segmentation mapfrom/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/ > dlab > el/mni/aparc+aseg.nii.gz > Loading b-valuesfrom/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/ > dmri > /bvals > Loading gradientsfrom/disks/open/judit/subjects/diffusion_tutorial/dtisubjects2005/subj_501/ > dmri > /bvecs > Segmentation fault > Linux Odd 2.6.35-28-generic #50-Ubuntu SMP Fri Mar > 18 18:42:20 UTC 2011 > x86_64 GNU/Linux > > trac-paths exited with ERRORS at Fri Oct 7 10:21:20 > CEST 2011 > > thanks for help. > Judit > > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > > > 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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Trouble downloading tutorial data
by Vy Dinh 26 Jul '12

26 Jul '12

Dear surfers, I'm having trouble downloading the longitudinal data form the website. This is the command I used: curl -O ftp://surfer.nmr.mgh.harvard.edu/pub/data/long-tutorial.tar.gz Error message: curl: (56) FTP response reading failed Am I typing the filename in wrong? Also, I tested the command to download another file and it work, but not for the longitudinal data. Thanks, Vy

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Re: [Freesurfer] stats
by Douglas N Greve 26 Jul '12

26 Jul '12

Hi Viola, I have a different work flow for you. When you run FDR, it will change the "Min" value under "Threshold". Go to a terminal and cd to the contrast directory of your qdec output folder, then run the commands below. It is assumed below that the threshold you want to use is 3.37. You should replace that with the threshold found by FDR. The files with the "337" can be named anything. I just put "337" to make them unique. doug cd QDECOUTPUTDIR/CONTRAST mri_surfcluster --in sig.mgh --thmin 3.37 --subject fsaverage --hemi lh \ --sum cluster.337.summary.dat --ocn cluster.337.seg.mgh \ --annot aparc --oannot ./cluster.337.seg.annot mri_segstats --seg cluster.337.seg.mgh --excludeid 0 --i ../y.mgh \ --sumwf cluster.337.wf.dat cluster.337.wf.dat will be a text table with number of rows equal to the number of subjects and number of columns equal to the number of clusters. To see which cluster is which, run tksurfer fsaverage lh inflated -annot ./cluster.337.seg.annot -curv -gray Each cluster will have a color and a number. On 07/24/2012 02:52 AM, Oertel, Viola wrote: > Okay. And how I do the clusterwise correction? In which window does it appear? > > Viola > > ________________________________________ > Von: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu]" im Auftrag von"Douglas Greve [greve(a)nmr.mgh.harvard.edu] > Gesendet: Dienstag, 24. Juli 2012 04:06 > Bis: Oertel, Viola; free surfer > Betreff: Re: [Freesurfer] stats > > Neither of these tables is the one you want. Those are tables of > standard freesurfer ROIs and are unrelated to your map-based analysis. > You will need to do the cluster-wise correction for multiple comparisons > using the voxel-wise threshold that FDR found. Set the cwp (cluster-wise > p-value) threshold to 1 so that you get all of the clusters. When you do > the clusterwise correction, it will produce a file with the values you want. > doug > > On 7/23/12 2:44 AM, Oertel, Viola wrote: >> Hi Doug, >> I did the correction for multiple comparisons (FDR 0,05). Then, I have seen significant clusters in the map. After that, I run the generate tables stat (or so on) button and got two tables with thickness values. But I don't know which one of the tables is the right one because this step produced two files: >> >> >> lh.aparc.a2005s.thickness.stats and >> lh.aparc.thickness.stats >> >> May you tell me which one is the right, and are these results only the significant areas, or all computed once? >> >> >> Thanks, >> Viola >> >> ________________________________________ >> Von: Douglas N Greve [greve(a)nmr.mgh.harvard.edu] >> Gesendet: Freitag, 20. Juli 2012 21:26 >> Bis: Oertel, Viola; Freesurfer(a)nmr.mgh.harvard.edu >> Betreff: Re: AW: [Freesurfer] stats >> >> Hi Viola, those stats tables are unrelated to your map-based exploratory >> analysis. If you have clusters in your map, you should run the >> correction for multiple comparisons. This will give you significant >> clusters. It will also produce a table of mean thicknesses in each >> cluster for each subject which you can then import to SPSS. >> doug >> >> On 07/19/2012 04:35 PM, Oertel, Viola wrote: >>> Yes. I did the contrast pat. vs. cont and see some significant regions on the display. After that, I did this "generate" stats table. My idea was to put this scores into SPSS and run the inferential statistics there. But I am not sure which table I have to use. What I want to use are the thickness values of each participant of all significant regions which I can see on the template. >>> Currently, I am not sure what kind of regions the tables show? Are that all regions, only the significant ones of the specific contrast I compute? I have seen that both tables show different regions. But I currently don't how the selection works. >>> >>> May you help with that? >>> >>> Thanks and best regards, >>> >>> Viola >>> >>> ________________________________________ >>> Von: freesurfer-bounces(a)nmr.mgh.harvard.edu [freesurfer-bounces(a)nmr.mgh.harvard.edu]" im Auftrag von"Douglas N Greve [greve(a)nmr.mgh.harvard.edu] >>> Gesendet: Donnerstag, 19. Juli 2012 17:30 >>> Bis: freesurfer(a)nmr.mgh.harvard.edu >>> Betreff: Re: [Freesurfer] stats >>> >>> Those stats tables just gives statistics (means, standard deviations) >>> for thickness in different regions. They do not have inferential >>> statistics. Have you run an analysis on patients vs controls? >>> doug >>> >>> On 07/19/2012 09:27 AM, Oertel, Viola wrote: >>>> Dear Doug, >>>> >>>> I have a question: when I create the stats tables, there are two tables: >>>> >>>> lh.aparc.a2005s.thickness.stats and >>>> >>>> lh.aparc.thickness.stats >>>> >>>> which one is the right one if I want to get the thickness values of >>>> the significant clusters from the main effect (pat. / controls)? >>>> >>>> Thanks and best regards, >>>> >>>> Viola >>>> >>>> >>>> >>>> _______________________________________________ >>>> Freesurfer mailing list >>>> Freesurfer(a)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 >>> Phone Number: 617-724-2358 >>> Fax: 617-726-7422 >>> >>> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >>> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >>> >>> _______________________________________________ >>> Freesurfer mailing list >>> Freesurfer(a)nmr.mgh.harvard.edu >>> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >>> >>> >>> 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 >> Phone Number: 617-724-2358 >> Fax: 617-726-7422 >> >> Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting >> FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html >> >> > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)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 Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html

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Surface number of vertices mismatch
by Pablo Polosecki 26 Jul '12

26 Jul '12

Dear List, I am trying to show my results on Caret's F99 atlas, in Caret. For this I already managed to take my anatomical (white, pial etc) surfaces and register them to F99 in Caret, which works fine. I am trying now to get my functional p-map (initially a nifti volume) into Caret too to overlay them on my anatomical surface together with the atlas information. For this my plan s the followign 1-Convert my nifti p-map volume into a surface using mri_vol2surf 2-Convert the resulting surface into caret surface using caret_command tools. 3-Apply to the resulting surface the same transformation I applied to my anatomical surfaces to have them all in register with Caret's F99 atlas. It seems like step 1 works fine, but when I try to run step too, Caret complains that my anatomical surface doesn't have the same number of vertices as my functional surface. Indeed, when opening the anatomical surface in maltab with read_surf, it seems to have exactly twice the number of vertices that my functional surface has (I cannot open it with read_surf for some reason but I see the number when I open it with a text editor or when I look at the output of mri_vol2surf). Would anyone have a suggestion as to why this is the way it is and how I could have my 2 surfaces have the same number of nodes? Thank you very much, Pablo

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FW: bringing surfaces from different subjects into the same space in matlab
by Rebelo Ferreira Marques Jose Pedro 26 Jul '12

26 Jul '12

Dear freesurfer experts, I would like to know how to have paint surfaces (.w) from different subjects into a common surface (fsaverage for example) and/or would like to know if my current approach is correct: I have first used the general "recon-all" step on some T1-w images. Subsequently I used "mris_expand" to create the different surfaces at different depths. with "mri_vol2surf" I was able to obtain the T1-w images in the various surfaces. At that moment my different subjects surfaces had different number of vertices and I would like to average them together. Using matlab, read_surf, I loaded the coordinates in the sphere of the subject data and of the fsaverage data. Subsequently I used the matlab function distributed with freesurfer, mesh_vertex_nearest, to find the nearest vertices of the subject sphere surface to those of the fsaverage surface. I then created a new paint surface where only those vertices were taken into account. Could I say that now all my subjects are co-registered and that I can use the PALS12.annot distributed with fsaverage to extract the properties of the different Brodmann areas? Is there a better way to do this? Thanks in advance, Jose Marques

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CSF segmentation and cortical ribbon
by Christopher Coello 26 Jul '12

26 Jul '12

Dear Freesurfer users, I have been using the function mri_watershed with options -LABEL and -atlas to segment into csf, scalp and skull. This option also gives a segmentation of the gm and wm. All voxels of the head are assigned to one of the labels. Nevertheless, the segmentation obtained in the file aseg.mgz of the cortical ribbon is of much better quality the fast mri_watershed -LABEL one. The problem is now if I use the csf obtained with mri_watershed -LABEL together with the aseg.mgz gm segmentation, some voxels in the border between cortical ribbon and csf are unassigned. My question is then : how could I generate a csf map like the one obtained with mri_watershed -LABEL, but that is complementary of the segmentation present in aseg.mgz of the cortical ribbon ? Thanks a lot in advance, Best, -- Christopher Coello, Ph.D. Preclinical PET/CT unit http://www.med.uio.no/imb/english/research/about/infrastructure/pet/ Institute of Basic Medical Sciences Faculty of Medicine, University of Oslo tel. +4745154516 -- Christopher Coello, Ph.D. Preclinical PET/CT unit http://www.med.uio.no/imb/english/research/about/infrastructure/pet/ Institute of Basic Medical Sciences Faculty of Medicine, University of Oslo tel. +4745154516

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recon-all error
by Yigal Agam 25 Jul '12

25 Jul '12

Hi, We're getting the following error from recon-all: command line: pbsubmit -m etanski -c 'recon-all -s DODASD012 -all -i /cluster/archive/300/siemens/TrioTim-35006-20120718-151622-227000/391000-000015-000001.dcm -mail etanski(a)nmr.mgh.harvard.edu' output: ... ... mri_binarize --i ./tmp.mri_nu_correct.mni.14699/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.14699/ones.mgz $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ cwd /autofs/cluster/manoach/dod/subjects/DODASD012/mri cmdline mri_binarize --i ./tmp.mri_nu_correct.mni.14699/nu2.mnc --min -1 --o ./tmp.mri_nu_correct.mni.14699/ones.mgz sysname Linux hostname compute-0-88 machine x86_64 user etanski input ./tmp.mri_nu_correct.mni.14699/nu2.mnc frame 0 nErode3d 0 nErode2d 0 output ./tmp.mri_nu_correct.mni.14699/ones.mgz Binarizing based on threshold min -1 max +infinity binval 1 binvalnot 0 Found 16777216 values in range Counting number of voxels Found 16777216 voxels in final mask mri_binarize done mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.14699/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.14699/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14699/input.mean.dat $Id: mri_segstats.c,v 1.75.2.3 2012/07/16 14:41:02 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.14699/ones.mgz --i orig.mgz --sum ./tmp.mri_nu_correct.mni.14699/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14699/input.mean.dat sysname Linux hostname compute-0-88 machine x86_64 user etanski Loading ./tmp.mri_nu_correct.mni.14699/ones.mgz Loading orig.mgz Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 0 0 Reporting on 0 segmentations Computing spatial average of each frame Writing to ./tmp.mri_nu_correct.mni.14699/input.mean.dat mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.14699/ones.mgz --i ./tmp.mri_nu_correct.mni.14699/nu2.mnc --sum ./tmp.mri_nu_correct.mni.14699/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14699/output.mean.dat $Id: mri_segstats.c,v 1.75.2.3 2012/07/16 14:41:02 greve Exp $ cwd cmdline mri_segstats --id 1 --seg ./tmp.mri_nu_correct.mni.14699/ones.mgz --i ./tmp.mri_nu_correct.mni.14699/nu2.mnc --sum ./tmp.mri_nu_correct.mni.14699/sum.junk --avgwf ./tmp.mri_nu_correct.mni.14699/output.mean.dat sysname Linux hostname compute-0-88 machine x86_64 user etanski Loading ./tmp.mri_nu_correct.mni.14699/ones.mgz Loading ./tmp.mri_nu_correct.mni.14699/nu2.mnc Voxel Volume is 1 mm^3 Generating list of segmentation ids Found 1 segmentations Computing statistics for each segmentation 0 1 0 0 Reporting on 0 segmentations Computing spatial average of each frame Writing to ./tmp.mri_nu_correct.mni.14699/output.mean.dat (standard_in) 1: syntax error mris_calc -o ./tmp.mri_nu_correct.mni.14699/nu2.mnc ./tmp.mri_nu_correct.mni.14699/nu2.mnc mul Linux compute-0-88 2.6.32-220.23.1.el6.x86_64 #1 SMP Mon Jun 18 18:58:52 BST 2012 x86_64 x86_64 x86_64 GNU/Linux recon-all -s DODASD012 exited with ERRORS at Wed Jul 25 12:27:28 EDT 2012 For more details, see the log file /autofs/cluster/manoach/dod/subjects/DODASD012/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting Any suggestions? Thanks, Yigal

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non-stationarity in CTh maps
by Hugo Baggio 25 Jul '12

25 Jul '12

Dear all, I have been performing cortical thickness analyses and as far as I understand the thickness maps are non-stationary (please correct me if I'm wrong). I have two questions: 1. How susceptible is Monte Carlo clusterwise correction to this (should I expect clusters at smoother areas to be bigger?)? 2. Does FS perform some sort of correction to this non-stationarity or are images assumed to be stationary at statistical analyses? Thanks a lot for your help! Hugo

2 1

MRIread on matlab
by Kevin Chen 25 Jul '12

25 Jul '12

Hi all, I am a beginner to FreeSurfer, and have been experimenting with the MRIread function on MATLAB. I am able to load .nii files using MRIread, but is there a way to display a particular slice from a nifti file on MATLAB using MRIread and its related functions? Thanks in advance, Kevin

2 1

Re: [Freesurfer] Freesurfer Question
by Alexandra Tanner 25 Jul '12

25 Jul '12

Hi Doug, Yes, sorry about that! I realized after I'd sent the email to you that I should've sent the email to the freesurfer list as well. We were hoping to look at volume in subcortical regions of the brain -- basal ganglia, hippocampus, amygdala, etc. Do know if there are commands to do the within subjects paired analysis this way? And if so, what they are? Thanks so much! Alex > Hi Alexandra, what structure are you looking to analyze? Ie, the volume > of what? The volume of cortex? > doug > ps. In the future, please post such questions to the freesurfer list as > it gives others the opportunity to answer and to learn. thanks! > > On 07/23/2012 12:03 PM, Alexandra Tanner wrote: >> Hi Mr. Greve, >> >> My name is Alex Tanner, I'm the new CRC for Dr. Roffman in the Brain >> Genomics Lab. I had a question regarding conducting volume analyses. On >> the freesurfer wiki there are commands that show how to conduct Paired >> Analyses to look at average surface, and I was curious if it was >> possible >> to do a paired analysis looking at volume instead. >> Any information you have would be very helpful. >> >> Thanks so much! >> >> Best, >> >> Alexandra Tanner >> Clinical Research Coordinator >> Laboratory for Brain Genomics >> Division of Psychiatric Neuroimaging >> Massachusetts General Hospital >> 149 13th Street >> Charlestown, MA 02129 >> (p) 617.643.3215 >> >> > > -- > 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html > > >

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