Freesurfer September 2012

freesurfer@nmr.mgh.harvard.edu

89 participants
154 discussions

resending question about 3rd level analysis
by Susan Alice McLaughlin 05 Sep '12

05 Sep '12

Hi, I'm resending this e-mail, as it didn't seem to go through correctly yesterday: I’m a Freesurfer novice, and I’m confused about how to run a 3rd level cross-subject analysis on the surface using as input cross-run .gfeats from 10 subjects generated from a 2nd level analysis in FSL. Following the directions posted at http://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/FslGroupFeat, I have sampled the .gfeat copes and varcopes into standard surface space, using mris_preproc. I would then go on to perform a 3rd level surface based analysis as the instructions suggest, using: mri_glmfit --y xrun/lh.cope1.mgh --yffxvar xrun/lh.varcope1.mgh --ffxdof 163 --osgm --glmdir xrun/lh.osgm.ffx --surf fsaverage lh --label $SUBJECTS_DIR/fsaverage/label/lh.cortex.label However, I want to use a random as opposed to fixed effects analysis. How do I do this? I tried --yrfxvar as opposed to --yffxvar but it didn’t work. And if I’m going to display the map resulting from this analysis, do I need to correct for multiple comparisons? Many thanks in advance, Susan McLaughlin Doctoral Candidate SPACE Lab (Stimulus-Parametric Imaging of Auditory Cortex) Dept. of Speech and Hearing Sciences University of Washington

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Re: [Freesurfer] FDR Correction of NHP Surface Data
by Clark Fisher 05 Sep '12

05 Sep '12

Ok, maybe I'm making this question too intricate. Here's the short version: How can I FDR correct painted surface significance maps when I have no talraich .xfm file and no cortical segmentation? Thanks again, Clark Hi Freesurfers, I have another monkey-specific question. I'd like to output FDR-corrected signficance surface maps for my monkey data, or at least FDR-threshold the maps. It seems like mri_surfcluster might be one way to go about this however: 1) I don't have any .xfm files for my monkeys, as I'm working in native space, and 2) Without segmentation, I don't have a good mask to use for the cortex only. My first attempts at work-arounds would be: 1)Try to create an identity .xfm file 2)Use the cortical ribbons from mris_volmask as a cortex mask Should these work? If so, how should I make an identity .xfm file? If not, is there another way to FDR correct my surface data? Thanks, Clark _______________________________________________ Freesurfer mailing list Freesurfer(a)nmr.mgh.harvard.edu<mailto:Freesurfer@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-Error message
by Bruce Fischl 05 Sep '12

05 Sep '12

Is that the actual name of the file? Does it have a dcm extension? On Wed, 5 Sep 2012, Varghese, Chikku wrote: > Thanks Bruce, > Still no luck,this what I am getting > > > /freesurfer/subjects/test1> recon-all -i /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image00001.dcm -subjid test7 -all > Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 > Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 > INFO: SUBJECTS_DIR is /home/virtualuser/freesurfer/subjects > Actual FREESURFER_HOME /home/virtualuser/freesurfer > Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux > /home/virtualuser/freesurfer/subjects/test7 > > mri_convert /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image00001.dcm /home/virtualuser/freesurfer/subjects/test7/mri/orig/001.mgz > > mri_convert /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image00001.dcm /home/virtualuser/freesurfer/subjects/test7/mri/orig/001.mgz > file not found or unknown file type for file /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image00001.dcm > Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux > > recon-all -s test7 exited with ERRORS at Wed Sep 5 09:51:17 EDT 2012 > > For more details, see the log file /home/virtualuser/freesurfer/subjects/test7/scripts/recon-all.log > To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting > > FreeSurfer:~/freesurfer/subjects/test1> > > -----Original Message----- > From: Bruce Fischl [mailto:fischl@nmr.mgh.harvard.edu] > Sent: Dienstag, 4. September 2012 18:25 > To: Varghese, Chikku > Subject: Re: [Freesurfer] Freesurfer-Error message > > you need a -all at the end to tell it what to do. And please cc the list so others can answer! > > On Tue, 4 Sep 2012, Varghese, Chikku wrote: > >> >> recon-all -i >> /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image00001.dcm -subjid >> test4 >> >> Is it this command I should use? >> >> >> > > > 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-Error message
by Varghese Chikku 05 Sep '12

05 Sep '12

Thanks Bruce, Still no luck,this what I am getting /freesurfer/subjects/test1> recon-all -i /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image00001.dcm -subjid test7 -all Subject Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 Current Stamp: freesurfer-Linux-centos4-stable-pub-v5.1.0 INFO: SUBJECTS_DIR is /home/virtualuser/freesurfer/subjects Actual FREESURFER_HOME /home/virtualuser/freesurfer Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux /home/virtualuser/freesurfer/subjects/test7 mri_convert /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image00001.dcm /home/virtualuser/freesurfer/subjects/test7/mri/orig/001.mgz mri_convert /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image00001.dcm /home/virtualuser/freesurfer/subjects/test7/mri/orig/001.mgz file not found or unknown file type for file /media/sf_freesurferstudys/raw/raw_scr/T1pre/Image00001.dcm Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 01:57:59 UTC 2009 i686 GNU/Linux recon-all -s test7 exited with ERRORS at Wed Sep 5 09:51:17 EDT 2012 For more details, see the log file /home/virtualuser/freesurfer/subjects/test7/scripts/recon-all.log To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FreeSurfer:~/freesurfer/subjects/test1> On 4 September 2012 14:37, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> wrote: > if that's the name of the image file. Can you post the list on your > replies so others can answer? > > thanks > Bruce > > On Tue, 4 Sep 2012, Varghese Chikku wrote: > > Hi Bruce, >> Many thanks for you mail. >> Is this the command you referring to. >> recon-all -i /media/sf_freesurferstudys/**raw/raw_scr/T1pre/Image00001.**dcm >> -subjid test4 >> Thanks >> Chikku >> >> On 3 September 2012 17:33, Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> wrote: >> Hi Chikku >> >> you need to give it the path to an image file (any one will do) and >> it will figure out the other slices that makeup >> the same series. What is the resolution of your data? 50 slices >> isn't usually enough to cover the brain at high >> enough resolution to get good thickness results. >> >> cheers >> Bruce >> >> >> On Mon, 3 Sep 2012, Varghese Chikku wrote: >> >> >> Hi, >> >> While running the following command: >> >> recon-all -i /media/sf_freesurferstudys/**raw/raw_scr/T1pre >> -subjid test2 >> >> I keep seeing the following error: >> >> ... >> >> corRead(): can't open file >> /media/sf_freesurferstudys/**raw/raw_scr/T1pre/COR-.info >> $Id: mri_convert.c,v 1.179.2.1 2011/03/22 16:37:02 nicks Exp $ >> reading from /media/sf_freesurferstudys/** >> raw/raw_scr/T1pre... >> Linux FreeSurfer 2.6.28-11-generic #42-Ubuntu SMP Fri Apr 17 >> 01:57:59 UTC >> 2009 i686 GNU/Linux >> recon-all -s test2 exited with ERRORS at Fri Aug 31 04:20:28 >> EDT 2012 >> >> >> My image files, in dcm format, are at >> /media/sf_freesurferstudys/**raw/raw_scr/T1pre : >> >> /media/sf_freesurferstudys/**raw/raw_scr/T1pre> ls >> Image00001 Image00010 Image00019 Image00028 Image00037 >> Image00046 >> Image00002 Image00011 Image00020 Image00029 Image00038 >> Image00047 >> Image00003 Image00012 Image00021 Image00030 Image00039 >> Image00048 >> Image00004 Image00013 Image00022 Image00031 Image00040 >> Image00049 >> Image00005 Image00014 Image00023 Image00032 Image00041 >> Image00050 >> Image00006 Image00015 Image00024 Image00033 Image00042 >> Image00007 Image00016 Image00025 Image00034 Image00043 >> Image00008 Image00017 Image00026 Image00035 Image00044 >> Image00009 Image00018 Image00027 Image00036 Image00045 >> >> Many thanks for your help. >> chikku >> >> >> >> >> 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<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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missing ROI when using mri_label2vol to transfer ic2.tri
by Leon 05 Sep '12

05 Sep '12

Hi, folks when I transferred the annotation file obtained using mri_make_face_parcellation based on ic2 (162 labels) to a volume file using mri_label2vol, I found that one ROI patch was missing in the volume file (see attached). I searched archives and the closest thread I could found is that somebody reported an ROI with the last index was missing in the mgz file after they were transferred from the annotation file to the volume file. Could someone help on this? If this happens to be a bug, is there any other strategy that will allow me to get a GM/WM ribbon without a hole on it? Many thanks in advance Leon

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freesurfer tutorial data
by Dix.Meiberth＠ukb.uni-bonn.de 05 Sep '12

05 Sep '12

Dear sirs and madames, unfortunately I wasn't able to download the tutorial data for freesurfer. The download interrupted at 2 GB within the "bruckner_data_tutorial_subjs.tar.gz" I already did the recon_all process for 90 brains and wanted to improve my skills for the corrections. Is there any advise you can give to get the tutorial data? Best regards, Dix Meiberth (B.Sc. Neurowissenschaften) Funktionelle Bildgebung Klinik und Poliklinik für Psychiatrie und Psychotherapie Universitätsklinikum Bonn Sigmund-Freud-Strasse 25 53105 Bonn Tel. 0228-287-16366 Dix.Meiberth(a)ukb.uni-bonn.de

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repeated measures ANOVA with two groups
by Shannon Kogachi 05 Sep '12

05 Sep '12

Hi, Is there a way to set up a repeated measures ANOVA and ANCOVA with two different groups (ex: study group v. controls) and each subject has more than two timepoints? Would it be possible to assign each Input in the fsgd file to two classes (ex: timepoint scan and group) or is there another way to set up the fsgd file and contrast matrices? I've already used qdec in freesurfer 5.1 to calculate rates of change and symmetrized percent changes between the timepoints (using long_mris_slopes) but now would like to perform a repeated measures test. Thank you! -Shannon K.

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Cortical parcellations and probtrackx2 in diffusion space
by Alistair Perry 04 Sep '12

04 Sep '12

Hello freesurfer experts, I know this has been posted elsewhere with the original probtrackx. I am basically trying to create a surface file from the aseg+aparc.mgz cortical parcellation created when running recon-all. I wish to use this surface file as the seed reference file when performing probtrackx2. I have succeeded sucessfully in transforming the cortical parcellation into diffusion space, and have created a label file for it. However, I am having difficulty understanding converting the label file into ascii format, as required for probtrackx2. I am aware that you can convert a label file into ascii format using mri_convert, but you have to specify the lh.white surface file created when performing recon-all. This does not make sense to me for one this label file is not in diffusion space. Plus, why would I only specify one surface hemisphere when I have a label file that lists vertices across both hemispheres? In the end I am asking whether it is possible/and the best method in creating an ascii surface file of the whole cortical parcellation in diffusion space? Regards, Alistair

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creating a skull
by Borzello, Mia 04 Sep '12

04 Sep '12

Hi freesurfer family, I am trying to create the inner skull boundary and ran: mri_watershed -atlas - surf -useSRAS mri.nii brain However, after it finished running it said it was saving "brain", but "brain" was an unknown file type. Am i supposed to specify that somewhere? Thanks in advance, m

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error in long_mris_slopes command
by Shannon Kogachi 04 Sep '12

04 Sep '12

Hi Freesurfers, I've just tried to use the long_mris_slopes command on some longitudinal data. I've created my long.qdec.table.dat file. I've run this command before without any problems but I need to re-run it again. This time when I try to re-run it this error pops up: ERROR 1 : mris_label_calc intersect did not work? Is there any way to fix this? it also tells me the following: cp: target 'path/subjectID/lh.long.cortex.label' is not a directory Please let me know if there is any way to fix this. thank you!! -Shannon K.

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Freesurfer September 2012