Freesurfer

freesurfer@nmr.mgh.harvard.edu

16 participants
30084 discussions

Label to annot
by Wayne Su 28 Apr '09

28 Apr '09

I have the trouble to convert the BA label to annotation file. The Freesurfer 4.3.0 is on Mac OS 10.5.6. First, I got the BA label: mri_label2label --srcsubject fsaverage --srclabel fsaverage/label/lh.BA1.label --trgsubject 001 --trglabel 001/label/lh.BA1.label --hemi lh --regmethod surface This works. I can load the label onto the surface by using tksurfer. Select File->Label->Export Annotation. The Terminal window shows ³writing color table into annotation file...² and stop here. I checked the lh.BA1.annot, it¹s about 1MB. But when I try to load this annotation, the surfer warning me no lables imported and annotation was empty. I went to the command line and type in: mris_label2annot --s 001 --h lh --ctab 001/label/ba1.annot.ctab --l 001/label/lh.BA1.label --a BA1 Here is the message. subject 001 hemi lh SUBJECTS_DIR /Applications/freesurfer4.3/subjects ColorTable 001/label/ba1.annot.ctab AnnotName BA1 nlables 1 Loading /Applications/freesurfer4.3/subjects/001/surf/lh.orig 001/label/lh.BA1.label 001/label/lh.BA1.label 1 14465659 BA1 Mapping unhit to unknown Found 129453 unhit vertices Writing annot to /Applications/freesurfer4.3/subjects/001/label/lh.BA1.annot writing colortable into annotation file... This seems work because I can load the annotation onto the surface. But what are the ³unhit vertices²? Is this normal? The last question: how can I get the voxel number (volume) of this label? Thanks. Wayne

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recon-all settings
by Ed Gronenschild 28 Apr '09

28 Apr '09

Hi, I want to use parameters different from default for mri_nu_correct.mni. This command uses nu_correct for which I would like to set the following options: -distance 25 -stop 0.0001 -fwhm 0.1 These settings are more approriate when using 3T T1 data. How can I invoke these in recon-all? Can I use an options file? Ed

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is there a command to give resolution information?
by jake＠nmr.mgh.harvard.edu 28 Apr '09

28 Apr '09

Hi, This may be a frivolous question but I was just wondering if anyone knows a quick way to find out resolution of an image file, i.e., if I wanted to look at an older scan and wanted to check its resolution. I couldn't find any information in the wiki, but I may have just missed the correct area in my text search. Also, what if I wanted to confirm slice thickness? Thanks in advance! Jake

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Re: [Freesurfer] Comparison of cortical thickness results
by Nick Schmansky 28 Apr '09

28 Apr '09

Falk, If you have the .annot file for a subject, you can break that apart into individual label files using mris_annot2label. Then knowing which labels compose the parietal lobe (for the Desikan-Killiany atlas, superior and inferior parietal, supramarginal, precuneus and postcentral compose the parietal lobe), then you can create a new label file by combining the label files into one with a text editor (the second line is the number of vertices composing the label, so be sure to get that right). then use mris_anatomical_stats to get the stats on this new label. Nick On Mon, 2009-04-27 at 16:31 +0200, Falk Lüsebrink wrote: > Hi everyone, > > > > I’d like to compare the individual cortical thickness results of > Freesurfer with the results of another software. The other software > measures the cortical thickness for example across the whole left > parietal lobe. So I have to get the according value of the whole left > parietal lobe of Freesurfer’s results. But I don’t know exactly how to > do that. > > > > Does someone have any suggestions how to get this value? At first > glance I would weight the average thickness of every structure > belonging to the parietal lobe given in the aparc.a2005s file by the > number of vertices (or maybe the gray matter volume in case the volume > had a resolution of 1mm^3?). Sum everything up and divide it by the > number of vertices to get the mean average across the parietal lobe. > Would that result in the value I’m searching for? > > > > Thanks in advance, > > Falk > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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mris_preproc really averages?
by Jeff Sadino 27 Apr '09

27 Apr '09

Hello, I think my message got scrubbed from my last post with the pictures. I ran mris_preproc on 56 subjects and then graphed the concatenated image. I also read this image into matlab and did the averaging using matlab, and then graphed the resulting image. When I did this, the two average pictures were slightly different. I thought that mris_preproc just simply averages all the subjects into common space. I noticed that its vector in matlab keeps the thickness value for all vertex's for all 56 subjects. I want to have the matlab capability for some custom processing I am doing, but the discrepancy leads me to think that mris_preproc is not a simple average. Can anyone elucidate this for me? Thank you! Matlab script. Only place I would suspect a wrong assumption is when I throw out the rest of the subjects at curv4=curv3(1,:,:,1) %Select your input thickness file path='/mnt/users/Jeff/fs/lc/HIV/pass2pics/416/diff/nc.rh.ave.mgh'; %Read the thickness file curv=MRIread(path); %Select the volume attribute curv2=curv.vol; %Create a duplicate thickness array for manipulation curv3=curv2; %Get the number of concatanated subjects tmp=size(curv2); m=tmp(4) clear 'tmp' %Sum each vertex for all your subjects for im=2:m for in=1:7 curv3(1,:,in,1)=curv3(1,:,in,1)+curv2(1,:,in,im); end end %Select just the first frame curv4=curv3(1,:,:,1); %Compute the average thickness curv.vol=curv4/m; %Write to thickness file MRIwrite(curv,'nc.rh.ave1.tmp.mgh'); _________________________________________________________________ Windows Live™ SkyDrive™: Get 25 GB of free online storage. http://windowslive.com/online/skydrive?ocid=TXT_TAGLM_WL_skydrive_042009

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mri_convert problem
by Rodrigo Zepeda 27 Apr '09

27 Apr '09

Hi, I'm trying to run mri_convert to convert CT dicoms into nifti format but I keep getting the following error: [multnomah:CT] (nmr-std-env) mri_convert -i 1.2.840.10008.5.1.4.1.22342498128.100.dcm -o ct.nii mri_convert -i 1.2.840.10008.5.1.4.1.22342498128.100.dcm -o ct.nii file not found or unknown file type for file 1.2.840.10008.5.1.4.1.22342498128.100.dcm I'm running this from /autofs/space/multnomah_002/users/Cashlab/MG13/CT. I think the sources and directory are OK because I ran mri_convert to convert this same subject's MRI into mgz without problems. Is there a problem with the dicoms format then? How can I bypass this? Thanks!

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mris_glmfit annotation error
by Devdutta W 27 Apr '09

27 Apr '09

Hi, While going through the annotation of the clusters, we noticed that the regions that the cluster summary prints out do not correspond to the actual location in the brain. For example, in the summary one of the clusters is reported to be in the isthmus of cingulate. However, when I look at the corresponding cluster on tksurfer it is quite clearly not medial (in fact it is on the temporal lobe). Has anybody encountered this problem before? If so, any idea why this is happening and how it can be fixed? I appreciate any help in this matter. Regards, Devdutta

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Re: [Freesurfer] White matter volumes for Gyrus and Sulcus
by Wayne Su 27 Apr '09

27 Apr '09

Sorry, I found the error in my script. The ctxseg option cannot be used here, and we should use a2005s option for mri_aparc2aseg command. Wayne On 27/04/09 10:25 AM, "Wayne Su" <wsu(a)interchange.ubc.ca> wrote: > Hello, > > Is there a way to get white matter volumes of gyrus and sulcus in Destrieux > atlas? I tried to use the same method used by white matter parcellation for > Desikan-Killiany atlas, but no wm volumes were reported. Or we get the total > volume of the label (how?), then subtract the gray volume to get white > volume? > > Thanks for any info. > > > Wayne > > > > > _______________________________________________ > Freesurfer mailing list > Freesurfer(a)nmr.mgh.harvard.edu > https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

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Convert image
by Kelly Silva 27 Apr '09

27 Apr '09

Hello, How can I convert one file *.label into *.img? Thanks in advance. Best regards, Kelly Veja quais são os assuntos do momento no Yahoo! +Buscados http://br.maisbuscados.yahoo.com

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RES: Re: Re: Re: [Freesurfer] Individual thickness data extraction from plot
by Pedro Paulo de Magalhaes Oliveira Junior 27 Apr '09

27 Apr '09

You are not doing it right. That script is to be run inside a script. Create a file try.sh paste that lines in try.sh Execute chmod +x try.sh Run ./try.sh good luck PPJ Sent from my Nokia phone @E71 -----Msg original----- De: Marina.Lopez(a)crccorp.es Enviada: 27/04/2009 06:00:30 Assunto: Re: Re: Re: RES: [Freesurfer] Individual thickness data extraction from plot Hi Nick and Pedro Paulo, Thanks a lot for your help and explanations. I have tried to do what you told me but still find only one asc file. I am copying to you what I did, just in case you could detect my mistake: (mailto:marina@linux4:~/FS$) marina@linux4:~/FS$ export SUBJECTS_DIR=/data/User/marina/FS Where my subjects data folders are (mailto:marina@linux4:~/FS$) marina@linux4:~/FS$ echo $SUBJECTS_DIR /data/User/marina/FS (mailto:marina@linux4:~/FS$) marina@linux4:~/FS$ #!/bin/bash Writing this will imply using bash? (mailto:marina@linux4:~/FS$) marina@linux4:~/FS$ cd qdec/LHTOTS_graficProva Where my specific qdec analysis was performed (from which plot data were extracted) (mailto:marina@linux4:~/FS/qdec/LHTOTS_graficProva$) marina@linux4:~/FS/qdec/LHTOTS_graficProva$ set numsubject = 53 my number of subjects in this analysis (mailto:marina@linux4:~/FS/qdec/LHTOTS_graficProva$) marina@linux4:~/FS/qdec/LHTOTS_graficProva$ for i in `seq 1 $numsubject` > do > mri_convert --frame $i y.mgh ../../fsaverage/surf/lh.$i.mgh > mris_convert -c $i.mgh ../../fsaverage/surf/lh.inflated lh.$i.asc > done mri_convert --frame 1 y.mgh ../../fsaverage/surf/lh.1.mgh $Id: mri_convert.c,v 1.146.2.3 2008/08/11 22:18:58 nicks Exp $ reading from y.mgh... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, 0) j_ras = (0, 0, -1) k_ras = (0, 1, 0) keeping frame 1 writing to ../../fsaverage/surf/lh.1.mgh... reading group avg surface area 822 cm^2 from file (mailto:marina@linux4:~/FS/qdec/LHTOTS_graficProva$) marina@linux4:~/FS/qdec/LHTOTS_graficProva$ When I look for my asc files in LHTOTS_graficProva I only find lh.1.asc and the data inside this folder does not correspond to any of my subjects, as far as I have checked it. Thanks again for all your help! i really need it. Marina Av�s | Aquest correu i qualsevol fitxer adjunt existent, contenen informaci� confidencial que van dirigits �nica i exclusivament al seu destinatari. Queda totalment prohibit realitzar-ne c�pies, aix� com difondre el seu contingut a altres persones que no siguin les destin�taries. Aviso | Este correo y cualquier fichero adjunto existente, contienen informaci�n confidencial que va dirigida �nica y exclusivamente a su destinatario. Est� completamente prohibido hacer copias, as� como difundir su contenido a otras personas que no sean los destinatarios. This message and any files attached are confidential. It is intended solely for the use of the addressee(s). If you are not the intended recipient of this e-mail, please note that any review, dissemination, disclosure, alteration, printing, copying or transmission of this e-mail and/or any file transmitted with it, is prohibited and may be unlawful.

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Freesurfer