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30132 discussions

make a volume template from the surface-based template for non-human primates
by Longchuan Li 18 Mar '13

18 Mar '13

Hi, FreeSurfer experts I have a question regarding making a volume template based on the surface template for non-human primates. I have made a surface template using a group of monkeys and now, we want to see the result, which is a mgh surface file, on the coronal slices of the template. So I am planning to generate a volume template corresponding to the surface template and then project the mgh file to the volume for viewing. Could someone tell me what is the best way to generate such a volume template? Many thanks in advance! Longchuan

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Definition of medial temporal lobe
by Akshay 18 Mar '13

18 Mar '13

Hello freesurfer experts, I am doing some TBM analysis and I am looking for the definition of Medial temporal lobe. According to the definitions I found out they are hippocampus+amygdala+brainstem+parahippocampal regions+entorhinal region. I can get hippocampus and amygdala ROI from aseg.mgz; however for parahippocampal and entorhinal regions should i use aparc+aseg.mgz and aparc.a2009s+aseg.mgz? Any help will be appreciated. Best, Akshay

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Re: [Freesurfer] editing Cts an pial surface
by Claudia Dacquino 18 Mar '13

18 Mar '13

yes I'm sorry, I'm new here. thanks a lot. claudia 2013/3/18 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > Hi Claudia > > can you cc the list so others can answer? I would view the ?h.pial and > ?h.white surfaces over the norm.mgz and see if you think they are accurate. > If not, there are various interventions you can take to correct them, that > are detailed on our wiki > > > cheers > Bruce > > > On Mon, 18 Mar 2013, Claudia Dacquino wrote: > > Thaks a lot Bruce, >> so I have to edit WM first, and then, what about grey matter? Do I have >> to paint all the None Sgmtn label points, or just >> the >> ones incorporating a piece of dura (so the very external ones)? >> Thanks, >> Claudia >> >> 2013/3/18 Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> >> Hi Claudia >> >> the first thing to do is run recon-all -all to complete a recon. >> Then you look through your data (surfaces >> overlaid on volumes) and determine if it is accurate (or accurate >> enough). If not, then control points are >> one possible intervention, and yes you would put them in regions of >> non-partial-volumed WM in which the >> intensity is < 110. This can cause the pial surface to move out as >> well as the white surface, but there are >> other reasons things can go wrong also such as topological defects >> and such. >> >> cheers >> Bruce >> >> On Mon, 18 Mar 2013, Claudia Dacquino wrote: >> >> Hi everyone, >> I'm a very new fresurfer user and I have to understand the >> very simple basis of its use yet. >> So I have some maybe stupid questions about that. >> I heve to work on cortical thickness, so I suppose I have to >> complete the segmentation and then >> correcting CPs and Pial >> surface. >> The first question is if I have to edit CPs first and then, >> after running recon-all >> -autorecon2-cp -autorecon-3, to edit >> the Pial surface? >> The second is in the CPs editing have I to add ctrl pts in >> white matter areas that are less then >> 110 in voxel intensity? >> The last one is how do I have to correct the grey matter? >> Have I to paint all the None Sgmtn >> label points, or just the >> ones incorporating a piece of dura? >> Thanks a lot, and sorry for the very basic questions. >> >> >> >> 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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editing Cts an pial surface
by Claudia Dacquino 18 Mar '13

18 Mar '13

Hi everyone, I'm a very new fresurfer user and I have to understand the very simple basis of its use yet. So I have some maybe stupid questions about that. I heve to work on cortical thickness, so I suppose I have to complete the segmentation and then correcting CPs and Pial surface. The first question is if I have to edit CPs first and then, after running recon-all -autorecon2-cp -autorecon-3, to edit the Pial surface? The second is in the CPs editing have I to add ctrl pts in white matter areas that are less then 110 in voxel intensity? The last one is how do I have to correct the grey matter? Have I to paint all the None Sgmtn label points, or just the ones incorporating a piece of dura? Thanks a lot, and sorry for the very basic questions.

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question about hippocampus subfield segmentation flag
by Mehul Sampat 18 Mar '13

18 Mar '13

Hi Folks, I had a question about the hippocampus subfield segmentations as described here : http://surfer.nmr.mgh.harvard.edu/fswiki/HippocampalSubfieldSegmentation I am planning to use this processing outline: 1. recon-all -s <subject> -autorecon1 -autorecon2 2. add control points 3. recon -all -s <subject> -autorecon2-cp 4. recon -all -s <subject> -autorecon3 -hippo-subfields Is this permissible or do I need to need to introduce the -hippo-subfields flag earlier. Thanks Mehul

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long_qdec_table
by Christopher McCarthy 18 Mar '13

18 Mar '13

Hey All, I am trying to turn my long.qdec.table.dat into a cross.qdec.table.dat using the following command: long_qdec_table --qdec ./qdec/long.qdec.table.dat --cross --out ./qdec/cross.qdec.table.dat However, when I try and load it into QDEC afterwards I get the following error: Loading data table /data/freesurfer/qdec/cross.qdec.table.dat... Number of columns: 103 fsid column: 1 Number of factors: 102 Number of subjects: 0 ERROR: QdecDataTable::Load: number of subjects = 0 Error loading the data table. I attached both the long.qdec and the cross.qdec tables, if someone knows what I am doing wrong, I would love some help! Chris

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Re: [Freesurfer] Asymmetries of cortical thickness
by Douglas N Greve 18 Mar '13

18 Mar '13

It is possible, it is just not a good idea because if you map rh to lh and then compare to lh, the rh will have been interpolated to get it into the lh. Even if there are no differences between the two, you will see differences because of the interpolation. Mapping both to fsaverage_sym means that both will be interpolated. If this interpolation does not bother you, then I can show you how to get it from rh to lh. doug On 03/18/2013 09:24 AM, Sophie Maingault wrote: > So i didn't understand what you mean by "just specify one subject when your > mris_preproc" ? Because, in fact I don't want to use the registration on > fsaverage_sym. I would like just to create a file lh.thickness less > rh.thickness vertex per vertex, maybe it is not possible ? > > -----Message d'origine----- > De : Douglas N Greve [mailto:greve@nmr.mgh.harvard.edu] > Envoyé : lundi 18 mars 2013 14:15 > À : Sophie Maingault; Freesurfer(a)nmr.mgh.harvard.edu > Objet : Re: [Freesurfer] Asymmetries of cortical thickness > > No, it is not, the target needs to be fsaverage_sym > doug > > > On 03/18/2013 09:13 AM, Sophie Maingault wrote: >> So I do : mris_preproc --target fsaverage --xhemi --hemi lh --paired-diff >> --meas thickness --out lh.lh-rh.thickness.sm00.mgh --s t0001 --s t0003 --s >> t0009 --s t0027 --s t0031 --s t0033 --s t0126 --s t0148 --s t0171 --s > t0174 >> --s t0199 --s t0203 --s t0212 --s t0215 --s t0242 --s t0245 --s t0253 --s >> t0254 --s t0256 --s t0268 >> >> You think it's ok ? >> >> Sophie >> >> -----Message d'origine----- >> De : freesurfer-bounces(a)nmr.mgh.harvard.edu >> [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] De la part de Douglas N >> Greve >> Envoyé : lundi 18 mars 2013 13:49 >> À : freesurfer(a)nmr.mgh.harvard.edu >> Objet : Re: [Freesurfer] Asymmetries of cortical thickness >> >> you will have to use the same stream, just specify one subject when your >> mris_preproc >> doug >> >> >> On 03/18/2013 08:06 AM, Sophie Maingault wrote: >>> Hello, >>> >>> Iobtained a map of cortical thickness asymmetries after the >>> registration on the symmetric atlas. But I would to obtain the same >>> map with raw data I mean just by subtract lh.thickness and >>> rh.thickness. How can I modify the part #Create a stack of subjects in >>> wiki page ? I have to register to fsaverage (and not fsaverage_sym) >>> and then do the same thing ? >>> >>> Thanks you for your help. >>> >>> Sophie >>> >>> >>> >>> _______________________________________________ >>> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Re: [Freesurfer] Asymmetries of cortical thickness
by Douglas N Greve 18 Mar '13

18 Mar '13

No, it is not, the target needs to be fsaverage_sym doug On 03/18/2013 09:13 AM, Sophie Maingault wrote: > So I do : mris_preproc --target fsaverage --xhemi --hemi lh --paired-diff > --meas thickness --out lh.lh-rh.thickness.sm00.mgh --s t0001 --s t0003 --s > t0009 --s t0027 --s t0031 --s t0033 --s t0126 --s t0148 --s t0171 --s t0174 > --s t0199 --s t0203 --s t0212 --s t0215 --s t0242 --s t0245 --s t0253 --s > t0254 --s t0256 --s t0268 > > You think it's ok ? > > Sophie > > -----Message d'origine----- > De : freesurfer-bounces(a)nmr.mgh.harvard.edu > [mailto:freesurfer-bounces@nmr.mgh.harvard.edu] De la part de Douglas N > Greve > Envoyé : lundi 18 mars 2013 13:49 > À : freesurfer(a)nmr.mgh.harvard.edu > Objet : Re: [Freesurfer] Asymmetries of cortical thickness > > you will have to use the same stream, just specify one subject when your > mris_preproc > doug > > > On 03/18/2013 08:06 AM, Sophie Maingault wrote: >> Hello, >> >> Iobtained a map of cortical thickness asymmetries after the >> registration on the symmetric atlas. But I would to obtain the same >> map with raw data I mean just by subtract lh.thickness and >> rh.thickness. How can I modify the part #Create a stack of subjects in >> wiki page ? I have to register to fsaverage (and not fsaverage_sym) >> and then do the same thing ? >> >> Thanks you for your help. >> >> Sophie >> >> >> >> _______________________________________________ >> 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: www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/

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Neuroimaging RA position available at VA Boston
by Huiting Liu 18 Mar '13

18 Mar '13

The Memory and Neuroimaging lab (PI: Scott M. Hayes; http://www.bu.edu/brainlab/) integrated with the Memory Disorders Research Center and Neuroimaging Research Center at VA Boston Healthcare System, is currently accepting applications for a full-time neuroimaging research assistant to begin in the summer of 2013. Primary duties will include the collection, processing, and analysis of structural and functional MRI data in older adults and patients with memory impairment. The research will focus on the examination of the neural correlates of memory, as well as the relationship between physical fitness and age-related cognitive and neural decline. Applicants should have a BA or BS in neuroscience, psychology, or computer science and familiarity with Unix/Linux, Matlab, FSL or FreeSurfer. Interested applicants should send a cover letter, CV (including references), course transcripts, and a writing sample (thesis or term paper) as a single PDF to neurolab(a)bu.edu.

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A question regarding high FA values when running DTI script
by Rotem Saar 18 Mar '13

18 Mar '13

Hi all, I run into somthing that seems odd to me and wanted to consult - I run the following script for getting the FA values from my DTI scans: 1) dt_recon --i /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/I00001.dcm --s FOLDER-NAME --o /usr/local/freesurfer/subjects/FOLDER-NAME/DTI --b /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvals.bval /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/bvecs.bvec 2) tkregister2 --s fsaverage --surf white --reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii.reg --mov /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa-tal.nii 3) tkmedit FOLDER-NAME orig.mgz -aux brain.mgz -seg wmparc.mgz -reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat -overlay /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii -fthresh 0.2 -fmax 1 4) mri_vol2vol --mov /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa.nii --targ /usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz --s FOLDER-NAME --interp nearest --o /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii --reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/register.dat 5) tkregister2 --mov /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_marsal.nii --targ /usr/local/freesurfer/subjects/FOLDER-NAME/mri/orig.mgz --reg /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.nii.reg 6) mri_segstats --seg /usr/local/freesurfer/subjects/FOLDER-NAME/mri/wmparc.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i /usr/local/freesurfer/subjects/FOLDER-NAME/DTI/fa_FOLDER-NAME.mask.nii --sum /usr/local/freesurfer/subjects/FOLDER-NAME/stats/all_stats_fa_FOLDER-NAME I got a table with all the FA values, for each segment, but I suspect a problem: I think that the values are too high (I set the threshold to 0.2-1), am I right ? I'm attaching the table I got, and to be specific, I'm very much interested in the Corpus-Colosseum values, which are high (not surprising) but when I wanted to validate with some other structures, like the "left putamen" I saw 0.53 which is to my opinion too high ? I would really appreciate if you can have a look at the table I attached here. Can u guide me regarding what I can do to solve the problem ? Is that any way to confirm that after the mask, I am left only with white matter ? Thanks ! Rotem

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