Freesurfer May 2010

freesurfer@nmr.mgh.harvard.edu

98 participants
145 discussions

autorecon2 failture
by Gabriel Go.Es. 28 May '10

28 May '10

Dear FreeSurfers I was running the autorecon2: recon-all -subjid -autorecon2 and it gives the following error message: Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux $Id: recon-all,v 1.133.2.57 2009/08/06 18:27:48 nicks Exp $ /root/trabajo/freesurfer/bin/recon-all PWD /root/trabajo/freesurfer/subjects/MP2RAGE_2/mri CMD mri_ca_label -align -nobigventricles norm.mgz transforms/talairach.m3z /root/trabajo/freesurfer/average/RB_all_2008-03-26.gca aseg.auto_noCCseg.mgz saving intensity scales to aseg.auto_noCCseg.label_intensities.txt Linux localhost.localdomain 2.6.9-34.ELsmp #1 SMP Thu Mar 9 06:23:23 GMT 2006 x86_64 x86_64 x86_64 GNU/Linux recon-all exited with ERRORS at Fri May 28 14:57:45 CEST 2010 the autorecon1 was perform by using the flag -no-wsgcaatlas for skullstripping you may find attached the recon-status log for any information you may need any suggestions and help will be so appreciated Best Gabriel _________________________________________________________________ ¿Quieres conocer trucos de Windows 7? ¡Los que ya lo usan te los cuentan! http://www.sietesunpueblodeexpertos.com/index_windows7.html

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GM and thickness
by Kelly Silva 28 May '10

28 May '10

Hello, I'm doing regression analyses with cortical thickness at the level of voxel. Should I correct the total GM volume by introducing this parameter as a confounding variable? Shoud I include the intracranial volume as an additional nuisance variable? If positive, I assume that these variables can only be introduced as covariates if they differ between groups. Am I correct? I saw in one message that we should not corret for thickness. Why not? Thanks in advance and best regards, Kelly

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monkey segmentation error query
by Jason Connolly 28 May '10

28 May '10

Dear Freesurfer experts, We are attempting to segment a template monkey brain. The following is the command line input: recon-all -i /usr/local/freesurfer/subjects/template_2/mri/orig/MonkTempl_w81096_T1.nii.gz -s template -all -notal-check -force -noaseg It runs for a few hours and then we get the following error: "cannot find seed region for corpus collosum" Do we have to manually mark this somehow in tkmedit? Any advice would be appreciated! Thank you, Jason.

2 1

data conversion
by Yvonne.Fonken＠mpi.nl 28 May '10

28 May '10

Hi all, I've just started using Freesurfer and the software works fine (with .mnc extensions). However, my data has a .mri format. I couldn't find how to convert this data with Freesurfer. Does anyone know whether this format is supported within Freesurfer of how to convert it to a format that can be used in Freesurfer? Best wishes, Yvonne Fonken

2 1

Number of orig volumes
by pikase＠tin.it 28 May '10

28 May '10

Hi everyone, maybe this is a trivial question but I didn't find an answer in the archives, so I'll post it anyway. I've noticed in articles on cortical thickness using freesurfer that the number of initial T1 volumes (orig) is quite variable, ranging from 1 to 3 or 4. We are planning to evaluate the cortical thickness for a large sample (30/40 subjects), and we have 1 volume for each subject (3T, 200 slices. 1mm). I was wondering whether using a single volume could affect the results. However, I've already processed 15 subjects and the results look nearly perfect to me. Best regards Laura

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Mask with different contrasts in tksurfer
by caspari＠clipper.ens.fr 28 May '10

28 May '10

HI! Is it possible do generate masks out of two (or more) different overlays ( name.w file)/ contrasts, to then in the end display the overlapping acitvation in a new overlay? The aim would be to get/create ROIs/Labels, which are already masked for plotting their timecourses. How could this work for the single subject? I hope someone has an idea??? I'm already a bit desesperate.. Thanks a lot- Natlaie

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using mris_make_template
by Danny Kim 27 May '10

27 May '10

hello all, first time poster and apologize in advance if this question has been addressed previously.. can someone provide an example script of how to use the mris_make_template command? I am mainly confused about what the input should be and what the output should look like. I've tried: mris_make_template lh sphere.reg EP068 ./desktop/FS_EP068_TEMPLATE/lh_test.tif and it produced a .tif file at the output location but this doesn't look at all like the .tif files located in /Freesurfer/average folders. Any help would be appreciated. Thanks!! Danny Kim Brainmapping centre BC Children's Hospital 4480 Oak Street Vancouver BC Canada

1 0

mri_motion_correct.fsl buglet
by Sebastian Moeller 27 May '10

27 May '10

Dear Freesurfers, I just tried to use mri_motion_correct.fsl with the -tmpdir and -nocleanup options. Since I currently average around 10 to 16 mprage volumes per subject (NHPs) I want to look at the variance in addition to the average. And it seemed simplest to just keep the co-registered volumes in the tmpdir around and calculate the variance from those. But, it turns out that the -nocleanup does not work (nor does the implied -nocleanup that is set from -tmpdir (set CleanUp = 0)). The problem seems to be fixable by changing: cleanup: if($#CleanUp > 0) then foreach f ($CleanUpList) rm -f $f end endif rm -r $tmpdir goto cleanup_return; to: cleanup: if($#CleanUp > 0) then if (${CleanUp} == 1) then echo "cleaning up..." foreach f ($CleanUpList) rm -f $f end endif endif if (${CleanUp} == 1) then rm -r $tmpdir endif goto cleanup_return; or even simpler: goto cleanup; cleanup_return: to: if (${CleanUp} == 1) then goto cleanup; cleanup_return: endif it would be great if this could be included into the next version. (It would certainly make my life easier :)) Best Regards Sebastian

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aparc+aseg is all left cerebral white matter
by Elias Kersten 27 May '10

27 May '10

Hi, I am trying to run a subject through the entire recon-all pipeline. However, I noticed the second to last step, "-wmparc", was taking a very long time (days). Looking over the data, the aparc+aseg.mgz file is almost all labeled as "Left-Cerebral-White-Matter", including the background. Also, the lh.ribbon.mgz file appears like a series of speckles, while the rh.ribbon.mgz file looks normal. I'm not sure where this problem is originating from or what my next steps should be. Any suggestions? Thanks, Elias

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corpus callosum volumetry of some sagital slices only...
by Gonzalo Rojas 27 May '10

27 May '10

Hi: How can I get the volumetry of the corpus callosum in only some sagital slices ?... For example, 5 slices to the left and 5 to the right the medial line ?... Sincerely, Gonzalo Rojas Costa Laboratory for Advanced Medical Image Processing Department of Radiology Clínica Las Condes Lo Fontecilla 441, Las Condes, Santiago, Chile. Tel: 56-2-2105170 Cel: 56-9-97771785 www.clc.cl

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Freesurfer May 2010