Freesurfer June 2013

freesurfer@nmr.mgh.harvard.edu

170 participants
298 discussions

Monte Carlo simulation
by stdp82＠virgilio.it 05 Jun '13

05 Jun '13

Hi list, I performed Monte Carlo simulation on my cortical thickness analysis. Now, I have significant clusters in the map for p<0.05. Is possible to obstain form each significant cluster the real value of p? Thanks, Stefano

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hippocampal subfield segmentation
by Claudia Dacquino 05 Jun '13

05 Jun '13

Hi guys! I have a dataset including hippocampal subfields obtained through the -hippo-subfields flag. I want to have a measure of total hippo volume and I'm not sure which structures should I include in the sum. I was thinking to exclude fimbria and fissure and sum the others. Am I right? Or should I simply sum all the structures? Any help is more than welcome Cheers, Fabrizio

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Tracula
by stdp82＠virgilio.it 05 Jun '13

05 Jun '13

Hi list and Anastasia, I'm performing a set of data with tracula version 3.0. I have change my dmrirc file respect to previous analyses and now I have one problem "set: Variable name must begin with a letter.ERROR: must specify as many DWI dicoms as subjects". I do not find the line that is wrong. I think to have approximately used the same lines of previous and correct analysis. I have attached the configuration file. Note that I'm using nii.gz. Thanks and best regards. Stefano

2 1

processing flow
by Claudia Dacquino 05 Jun '13

05 Jun '13

Hi everyone, I'm sorry, this is a probably very basic question, but I'm a little bit confused about the recon-all correct flowchart. I mean, the first step is recon-all -s <subjid> -all (comprising autorecon1, autorecon2 and autorecon3), correct? After this step if I want to add control points then I have to re-run: recon-all -s <subject> -autorecon2-cp -autorecon3 The same if I want to edit pial surface: recon -all -s <subject> -autorecon2-pial -autorecon3 Or to edit white matter: recon-all -s <subject> -autorecon2-wm -autorecon3. Is that correct? Is there a system to reduce processing time once I've run eh first step (recon-all -s -all)? I mean if I want to add control points, then to edit pial surface and white matter, have I to do the three processes separately, or there is a way to do the three things at once and then running just one autorecon? If that is permissible, which is the correct command line at the end of the porcess? I'm sorry for the confusion. Thanks in advance to everyone. Claudia

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mri_mc vs. recon-all surfaces
by Oscar Esteban 05 Jun '13

05 Jun '13

Dear all, I need to extract three surfaces from MRI data: - GM-WM interface -> thus, lh.white and rh.white would be the answer. - Pial interface -> thus, lh.pial + rh.pial - CSF surface For CSF, as far as I know, the best option would be to generate a binary volume merging the appropriate labels from aseg.mgz. Then use mri_mc to obtain the surface, right? For white and pial I guess the best option would be to use the recon-all outcome, but I have two questions: * Is there any mean to merge both hemispheres? I've tried several methods but I get trouble with the consistency of the cells... the points are aggregated, but no work is done to merge cells and remove points. * What are the differences between the recon-all outcome (lh.pial,rh.pial,lh.white,rh.white) with respect obtaining masks from aseg.mgz and then mri_mc? Thank you so much Best regards, Oscar Esteban -- Oscar Esteban PhD Student / Researcher Biomedical Image Technologies (BIT), UPM ETSI Telecomunicación Lab. C203, Av. Complutense s/n - E-28040 Madrid (Spain) +34 915 495 700 ext.4234 Signal Processing Laboratory (LTS5), EPFL-STI-IEL-LTS5 ELD 224 (Bâtiment ELD), Station 11, CH-1015 Lausanne, Switzerland

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recon-all error
by 小麦 05 Jun '13

05 Jun '13

Hi experts, When I run recon-all,I met an error,the details are as follows. 1) the subject name is cwlzxm4 2) the entire command-line is recon-all -s cwlzxm4 -i /home/virtualuser/Desktop/raw/001.mgz -all 3)the recon-all.log is attached Thank you in advance, Best wishes, Wily

2 1

error while running autorecon1 and autorecon2 in fs-v5.3
by Mehul Sampat 04 Jun '13

04 Jun '13

Hi Folks, I am running recon-all with -autorecon1 -autorecon2, -nomotioncor -notal-check -nonuintensitycor (this is with fs version 5.3) it almost runs through but toward the end, when mri_segstats is called I get the error message: .../mri/ribbon.mgz, -1): could not open file any ideas why this could be occurring ? Thanks Mehul

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longer run time on 5.3 versus 5.2 ?
by Mehul Sampat 04 Jun '13

04 Jun '13

In some cases, we are seeing that, for the same subject, the run time is slower for 5.3 versus 5.2; A quick check on recon-all-status.log shows that the CA Reg Inv step is taking longer with 5.3. recon-all-status.log from data processed with 5.2: #@# CA Reg Thu Jan 17 16:03:53 PST 2013 #@# CA Reg Inv Thu Jan 17 20:17:32 PST 2013 recon-all-status.log from data processed with 5.3 #@# CA Reg Mon Jun 3 19:46:37 PDT 2013 #@# CA Reg Inv Tue Jun 4 04:52:57 PDT 2013 Is this expected ? Or in your own testing are the recon-all processing times similar for 5.2 versus 5.3 ? The recon-all.log file for both cases are attached; Thanks Mehul

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mri_nu_correct.mni
by Cristian Paz 04 Jun '13

04 Jun '13

Dear FreeSurfers! I want to do bias correction on some T1 and T2 images. I have heard that you can do this by using mri_nu_correct.mni how should I use this command? I could not understand this (I am a beginner in FS) : https://surfer.nmr.mgh.harvard.edu/fswiki/mri_nu_correct.mni would it be something like : mri_nu_correct.mni -i <path-to-input-file> -o <path-to-where-output-file-should-be written + filename>? Thank you very much! Kind regards, Cris

1 0

Freesurfer error..recon-all fails
by Manish Dalwani 04 Jun '13

04 Jun '13

Hello Freesurfer's I am working on the MAC OS 10.8 and just recently installed the freesurfer on this server machine. I have checked the permissions to various and folders and they look ok to me. When I run the following command: recon-all -i MR1000200001.dcm -s test2 I get the following error server:anat_5214 manishdalwani$ recon-all -i MR1000200001.dcm -s test2 Subject Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 Current Stamp: freesurfer-Darwin-lion-stable-pub-v5.3.0 INFO: SUBJECTS_DIR is /Applications/freesurfer/subjects Actual FREESURFER_HOME /Applications/freesurfer Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64 /Applications/freesurfer/subjects/test2 \n mri_convert /Applications/freesurfer/subjects/anat_5214/MR1000200001.dcm /Applications/freesurfer/subjects/test2/mri/orig/001.mgz \n mri_convert /Applications/freesurfer/subjects/anat_5214/MR1000200001.dcm /Applications/freesurfer/subjects/test2/mri/orig/001.mgz -------------------------------------------------------------------------- ERROR: FreeSurfer license file /Applications/freesurfer/license.txt not found. If you are outside the NMR-Martinos Center, go to http://surfer.nmr.mgh.harvard.edu to get a valid license file (it's free). If you are inside the NMR-Martinos Center, make sure to source the standard environment. -------------------------------------------------------------------------- $Id: mri_convert.c,v 1.179.2.7 2012/09/05 21:55:16 mreuter Exp $ reading from /Applications/freesurfer/subjects/anat_5214/MR1000200001.dcm... Darwin server.imaging.private 12.1.0 Darwin Kernel Version 12.1.0: Tue Aug 14 13:29:55 PDT 2012; root:xnu-2050.9.2~1/RELEASE_X86_64 x86_64 recon-all -s test2 exited with ERRORS at Tue Jun 4 09:56:10 MDT 2013 For more details, see the log file /Applications/freesurfer/subjects/test2/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting I am attaching the log file as well, and would appreciate if people can help with this issue. Best Regards, Manish Dalwani

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Freesurfer June 2013