Freesurfer

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Re: [Freesurfer] Cortical thickness/surface area in volume-defined ROIs
by Anita van Loenhoud 02 Dec '13

02 Dec '13

Hi Bruce, Thank you for your response. Now at least I know what went wrong; I'll try your solution. Thanks! Anita

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Volume differences after corrections
by Garikoitz Lerma-Usabiaga 01 Dec '13

01 Dec '13

Hi list, I obtained cortical thickness and volumetric results before and after correcting them for defects. I just did some wm edits and mostly controls points in the top of the head (some subjects had less signal so I put control points in order to allow for a good surface reconstructions). When comparing the values: EXPECTED - Same volume values for subcortical structures, i.e.: same thalamic volume before and after - Different CT values in the edited areas and only for the edited subjects, i.e.: lh_paracentral_thickness - Different volumetric values only for the edited subjects in, for example: lhCortexVol, CortexVol, CorticalWhiteMatterVol NOT EXPECTED - Same values for EstimatedTotalIntraCranialVol. I was controlling thalamic values with the eTIV, (using Raz 2005's formula)*, but before and after correcting almost half of the subjects, obviously, I obtain the same results. - Should I use a different value other than the eTIV? - Is normal that the eTIV doesn't change but the rest of the values are changing? The brain is definitely different after the control points, it grows a little bit upwards. any information on this will be appreciated! thanks, Gari PS: * Volume (adj) = Vol(rawi)-b*(ICV(i)-mean ICV), where b is the slope of regression of an ROI volume on ICV

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Within group hemisphere comparison in QDec
by krista kelly 30 Nov '13

30 Nov '13

Hello, I need to do a within group hemisphere comparison to see if there are any hemisphere asymmetries in a patient group. I would like to do this in QDec or if possible, somehow do it in freesurfer without using Qdec. I asked this question two years ago and you mentioned that you were working on this and it should be available soon. Has there been any progress? Thanks! Krista

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how to recon-all multiple participants simultaneously? thanks
by chen kanwisher 29 Nov '13

29 Nov '13

Dear Freesurfers, I'd like to ask how could we recon-all multiple participants at the same time? My laptop has a 32G ram and a 8-core-intel-Core-i7 CPU, i expect it could speed up the surface construction by running several participants simultaneously. When i use the following command: 'foreach i (1 2 3....);recon-all -subjid sub$i -all -openmp8;end', each participant needs 4-5 hours. Although this is much faster than the typical time consumption as stated in freesurfer wiki, i notice only 3 out my 32G working memory is used under such command. So I am wondering if there are some other ways to make full use of the working memory and make the surface construction go even faster. I have tried to open 8 terminal windows, each for a separate participant, and for each window, the command was like this, 'recon-all sub01 -all openmp 8'. It turned out the analysis ran extremely slow, none of the subjects finished even after 36 hours, the CPU was 100% used, but still no more than 7 of the 32G working memory was occupied. So, question, is it possible for me to make the analysis more quickly, and if so, how？ Looking forward to your informations, and thank you a lot! Chen

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Re: [Freesurfer] Cortical thickness/surface area in volume-defined ROIs
by Anita van Loenhoud 29 Nov '13

29 Nov '13

Hi Rujing Zha, Click this link: http://freesurfer.net/fswiki/VolumeRoiCorticalThickness Anita

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Cortical thickness/surface area in volume-defined ROIs
by Anita van Loenhoud 29 Nov '13

29 Nov '13

Dear Freesurfer experts, I want to use volume-defined ROIs (obtained in a VBM study) to extract mean thickness and surface area, in a total group of 138 participants. I followed the tutorial 'Cortical Thickness of a volume-defined ROI'. I have a few questions regarding this analysis: 1. The volume-defined ROI (i.e. orange dot) appears normal on my avg152_T1 and fsaverage. After the vol2surf-step, however, a few problems arise. The new ROIs look very different: one ROI actually consists of two clusters close to each other, one is very small and two ROIs have completely disappeared. Does anyone know why this happened? 2. When I want to obtain surface area data instead of thickness data, is it sufficient to replace 'thickness' with 'area' in the surf2surf command (it seems to work, but I want to check)? So: --sval lh.area \ --tval lh.area.fsaverage.mgh \ 3. mri_segstats creates separate files for each ROI in each participant. When I want to have all thickness and area ROI data in one file, can I use asegstats2table, meas mean (it seems to work, but I want to check)? Any help would be very much appreciated! Anita

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nii format input for recon-all
by Rujing Zha 29 Nov '13

29 Nov '13

Dear all, I have done the recon-all for DICOM format input of all subjects. Part of subjects extracted brain volume not very perfectly. I want to use brain volumes nifti format which have strip the skull and neck well. My question is how to use the brain volume in nii format to segment and next recon-all analysis. Thanks. All the best. 2013-11-29 Rujing Zha

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Re: [Freesurfer] freeview, mris_preproc, mri_surf2surf, mri_glmfit: wrong home directory
by Douglas Greve 28 Nov '13

28 Nov '13

you don't need to supply the full path to the inputs of mris_preproc, but you must for the output of mris_preproc as well as the input and output of surf2surf and glmfit On 11/28/13 1:25 PM, Laura Taylor wrote: > Thanks, Bruce... > > Do you know if you also have to specify the full path for the location > of _input _/and /_output_ files in mris_preproc, mri_surf2surf, and > mri_glmfit? > > By default, when I ran the above programs, my output files were placed > in my computers home directory and not my freesurfer home directory (I > did not specify full pathnames). > > However, mris_preproc seemed to be able to read in my target > (--target) (fsaverage) without needing a full pathname, and > mri_surf2surf also seemed to be able to read in my subject (--s) > without needing a full pathname. > > Please let me know if I have this right (especially regarding reading > in input files). > > Thank you, > > Laura > > On Wed, Nov 27, 2013 at 11:53 AM, Bruce Fischl > <fischl(a)nmr.mgh.harvard.edu <mailto:fischl@nmr.mgh.harvard.edu>> wrote: > > Hi Laura > > freeview by default doesn't use any of the environment variables. > You need to give it the full path to the data you are trying to > visualize. It included your home dir in the path probably because > that was your pwd. > > cheers > Bruce > > On Wed, 27 Nov 2013, Laura Taylor wrote: > > Hi, > > I previously installed set-up and have successfully used > freesurfer to run > recon-all and visualize my results in tkmedit and tksurfer. > However when I > went to analyze my data and also view it in freeview I have > run into a > problem with what my home directory is considered for these > applications. > > When I try and load images in freeview from the command line I > get the > following error: > > -------- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 > -------- > Setting up environment for FreeSurfer/FS-FAST (and FSL) > FREESURFER_HOME /Data/freesurfer > FSFAST_HOME /Data/freesurfer/fsfast > FSF_OUTPUT_FORMAT nii.gz > SUBJECTS_DIR /Data/freesurfer/subjects > MNI_DIR /Data/freesurfer/mni > woodward@Bambi:~$ freeview -v B60/mri/braimmask.mgz > mghRead(/home/woodward/B60/mri/braimmask.mgz, -1): could not > open file > MRIread failed: Unable to read from > /home/woodward/B60/mri/braimmask.mgz > mghRead(/home/woodward/B60/mri/braimmask.mgz, -1): could not > open file > > This is because freeview is looking for my subject in the > computers home > directory (~) which is /home/woodward. > > I get a similar problem when I run i.e. mri_glmfit. When I > specify > > --glmdir lh.dx_age.glmdir, it places the output in my home (~) > (/home/woodward) directory and not in my FREESURFER_HOME > directory. > mris_preproc and mri_surf2surf also seems to be placing their > output in my > computers home directory. > > > I've looked in FreeSurferEnv.sh and I can't seem to find a > place to make any > changes. Please let me know if I can edit a path somewhere, > or if I need to > write out the full path for the mri_* programs and freeview. > > > Thank you, > > > Laura > > > > > > > > > > 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. > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Re: [Freesurfer] mris_calc recon-all problem
by Johnson, Eileanoir 28 Nov '13

28 Nov '13

It is happening on every subject; the disk isn't full. I checked the MRI folder, and some of the files (nu.mgz, brainmask.mgz) weren't outputted. For one participant who had also been processed on another computer I copied these files onto the cluster and it seems to run ok once these files are in the folder. I found a similar problem (https://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2013-January/027257.h…) and have asked the team who maintain the cluster to try this solution as I don't have the right permissions. Hopefully this will solve the issue. Thanks for your help, Eileanoir -----Original Message----- From: freesurfer-bounces(a)nmr.mgh.harvard.edu [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] On Behalf Of Rudolph Pienaar Sent: 28 November 2013 00:47 To: Douglas N Greve; freesurfer(a)nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_calc recon-all problem Not sure if it's relevant, but the syntax for mris_calc in this case is: mris_calc -o <outputFile> <file1> mul <file2> Your log is missing <file2> so the syntax doesn't make sense and mris_calc will fail... On 11/27/13, 18:10 , Douglas N Greve wrote: > > Does it happen on every subject? Any chance that the disk is full? > > On 11/27/2013 07:43 AM, Johnson, Eileanoir wrote: >> >> Hi there, >> >> I am currently trying to run freesurfer version 5.3.0 on a cluster >> and am encountering an error when running recon-all. >> >> The error is: >> >> Writing to ./tmp.mri_nu_correct.mni.2867/output.mean.dat >> >> mri_segstats done >> >> mris_calc -o ./tmp.mri_nu_correct.mni.2867/nu2.mnc >> ./tmp.mri_nu_correct.mni.2867/nu2.mnc mul >> >> Linux blue34 2.6.18-164.6.1.el5 #1 SMP Tue Oct 27 11:28:30 EDT 2009 >> x86_64 x86_64 x86_64 GNU/Linux >> >> recon-all -s 22057 exited with ERRORS at Wed Nov 27 12:31:54 GMT 2013 >> >> Does anyone know what might be causing recon-all to exit at this >> point? I have attached the full log file. >> >> Thanks, >> >> Eli >> >> Eli Johnson >> Research Assistant, Track-On >> UCL Institute of Neurology, Box 104 Queen Square, London, WC1N 3BG >> Tel:+44(0)207 242 0038 >> >> >> >> _______________________________________________ >> Freesurfer mailing list >> Freesurfer(a)nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer > -- Rudolph Pienaar, M.Eng, D.Eng / email: rudolph(a)nmr.mgh.harvard.edu MGH/MIT/HMS Athinoula A. Martinos Center for Biomedical Imaging 149 (2301) 13th Street, Charlestown, MA 02129 USA _______________________________________________ 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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Re: [Freesurfer] Freesurfer course troubleshooting presentation slides
by Douglas N Greve 27 Nov '13

27 Nov '13

Are these this right one? ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/freesurfer.fa… On 11/27/2013 03:55 AM, Janosch Linkersdörfer wrote: > Hi, > > thank you very much for providing the lectures of the last Freesurfer course as videos! I am just watching them, and it seem that the .ppt file provided for the troubleshooting lecture does not match the slides used in the video. > > It would be great if you could provide the slides used in the video! > > Thanks, > > J > _______________________________________________ > 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: 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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