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30132 discussions

mri_glmfit with pvr: how to include pvr in the fsgd file?
by Burzynska, Aga 03 Aug '11

03 Aug '11

Dear all, I am trying to make group level analysis of functional data on the surface and add per-vertex regressors (PVR, here: cortical thickness) into the design. When I view the results I have the feeling that the PVR is not really included in the model: I am using the command: mri_glmfit --glmdir lh_output --y cope1_lh_4D.mgh --fsgd Group1versusGroup2.fsgd --pvr lh.thickness.10.mgh --C Group1only_thickness.mat --C Group2only_thickness.mat --C Group1minusGroup2_thickness.mat --C Group2minusGroup1_thickness.mat --C Group1plusGroup2_thickness.mat where cope1_lh_4D.mgh contains the concatenated sig.mgh images from the fixed level analysis (combining the runs) for each participant fsgd file contains: GroupDescriptorFile 1 Title Group1versusGroup2 Class Group1 Class Group2 Input 1109 Group1 Input 1110 Group1 Input 1111 Group1 Input 1112 Group1 ... Input 2280 Group2 Input 2282 Group2 Input 2283 Group2 Input 2284 Group2 The PVR is a file containing thickness maps for each participant, concatenated in the same order as for the functional data. So there are 2 main regressors (1 factor, 2 levels), but the contrast files contain 3 regressors (the third one is the PVE), for instance: Group1minusGroup2_thickness.mat contains 1 -1 0. Does it look correct? Should the pvr regressor be included in the fsdg file? How can I do it? Thank you very much for your help, Cheers, Aga

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Problem loading nii
by Tax, C.M.W. 03 Aug '11

03 Aug '11

Dear Sir/Madam, I would like to use freesurfer for cortical flattening, working with the nii format. When I try to load the nii.gz file as described on http://www.fmrib.ox.ac.uk/fsl/freesurfer/index.html, I get the following error: student@BMT-PC125:~$ tkmedit -f t1.nii.gz niiRead(): error opening file ./t1.nii.gz Error: Loading volume t1.nii.gz Couldn't read the anatomical volume. Tkmedit couldn't read the volume you specified. This could be because the image format wasn't recognized, or it couldn't find the proper header, or the file(s) were unreadable, or it was the wrong size. This image t1.nii.gz was obtained by converting DICOM images with dcm2nii. I also tried to load a example dataset downloaded from http://nifti.nimh.nih.gov/nifti-1/data, but still I get the same error. FSL was able to load both datasets without problems. Please could you help me with this problem? Thank you in advance, Kindest Regards

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isxconcat-sess missing dof file
by Chindhuri Selvadurai 03 Aug '11

03 Aug '11

Hi all, When I run isxconcat-sess, I am experiencing an error finding a 'dof' file in my analysis directories within the FSD files. subjects directory: /cluster/manoach/milton/subjects command line: isxconcat-sess -sf sessid_all -analysis mstmct_v_base -c type_v_rest_vol -o /cluster/manoach/milton/subjects/group_analysis/volume/ output: /cluster/manoach/milton/subjects/group_analysis/volume//mstmct_v_base/log/isxconcat.log ERROR: cannot find /autofs/cluster/manoach/milton/subjects/PAMST02/bold/mstmct_v_base/dof Did I miss a step before the isxconcat? Thank you!

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Re: [Freesurfer] Error with aparcstats2table
by Antonella Kis 03 Aug '11

03 Aug '11

Hi Bruce, Sorry to bother you again with the same question. Unfortunately I did not get any reply from the freesurfer list (from Doug and/or Nick as you mentioned) so I will really appreciate if you can help me with the same question:in the aparc stats I have for each segmentation the Number of Vertices, Surface Area, etc. I want this data to be exported in a table where in the first ro I will have the thickness of each segmentation(bankssts , etc) and the second row I want the Number of Vertices, for each subject. Many thanks, Antonella ________________________________ From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> To: Antonella Kis <atorok9(a)yahoo.com> Sent: Friday, July 29, 2011 5:24 PM Subject: Re: [Freesurfer] Error with aparcstats2table doug and nick can help with that On Fri, 29 Jul 2011, Antonella Kis wrote: > Hi Bruce, > > Thanks again for helping. I mean in the aparc stats I have for each segmentation the Number of Vertices, Surface Area, etc. I want this data > to be exported in a table where in the first ro I will have the thickness of each segmentation(bankssts , etc) and the second row I want the > Number of Vertices, for each subject. > > Thanks. > Antonella > > _______________________________________________________________________________________________________________________________________________ > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > To: Antonella Kis <atorok9(a)yahoo.com> > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Sent: Friday, July 29, 2011 3:18 PM > Subject: Re: [Freesurfer] Error with aparcstats2table > > Hi Antonella, > > what do you mean by no. of vertices? The total # in the surface? You can get that with mri_info. It's loosely related to surface area, but not > that interested a quantity. > > Bruce > > > On Fri, 29 Jul 2011, Antonella Kis wrote: > > > Hello everyone, > > > > > > I was trying to create a table with my statistical results (the cortical thickness and the number of vertices) and I was running: > > > > aparcstats2table --hemi lh --subjects bert NPI001 --meas thickness -t lh.aparcstas.THICKNESS.txt > > > > When I tried to also get the number of vertices a table by running: aparcstats2table --hemi lh --subjects bert NPI001 --meas vertices -t > > lh.aparcstas.VERTICES.txt I got the following error: > > > > aparcstats2table: error: option --measure: invalid choice: 'Voxels' (choose from 'area', 'volume', 'thickness', 'thicknessstd', 'meancurv') > > > > I Why I don't have an option for the no. of vertices? > > > > Can I get a table with both data: cortical thickness and no. of vertices? > > > > Many thanks, > > Antonella > > > > > > > > > > > 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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Rejoindre mon réseau sur LinkedIn
by Yuko Yotsumoto via LinkedIn 03 Aug '11

03 Aug '11

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mri_glmfit
by Mandy Nagy 02 Aug '11

02 Aug '11

One of our volume analyses does not look as it should after we perform the mri_glmfit. Our block design paradigm has 2 separate sessions for each subject with alternating periods of task and rest. We did individual analyses for task-rest for each session. We then concatenated the data into 2 files: one for each session. Then we ran fscalc to add the 2 concatenated files. Up until this point, the data looked like it should. subjects dir: /cluster/manoach/milton/subjects freesurfer 5 However, when we then ran the group analysis using mri_glmfit, we got results that looked abnormal. Our command: mri_glmfit --y mstmct_v_base.nii --glmdir group_analysis/volume/mstmct_v_base/ --osgm We were unsure if we should put in the fsgd file, because we weren't sure which subjects should be included because we added the two sessions using fscalc. (Each subject has two sessions and 2 subject IDS). We realize it could be a problem that arose before the mri_glmfit , but we aren't sure if there was anything else we should consider when running the mri_glmfit itself. Thank you!

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Tracula's sensitivity to recon version
by Shanqing Cai 02 Aug '11

02 Aug '11

Hi, While using traclua, I came across the following problem: it seems to me that the results of tracula are quite sensitive to the version in which the surface reconstruction is done. Please see the attached image. In those examples, both the shape and the size of the same tract of the same subject is different by a lot depending on whether version 5.0.0 or 5.1.0 is used for doing recon-all. As a consequence, the stats generated by Tracula, such as tract mean FA, volume, etc., are also dependent on recon version. I wonder whether this is because I did anything wrong in using tracula? Is this kind of version sensitivity expected? If so, which result should I trust? Thanks a lot! Best regards, Shanqing

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processing OASIS database using freesurfer 5
by Gonzalo Rojas Costa 02 Aug '11

02 Aug '11

Hi: I need to reprocess some images of the OASIS database using freesurfer 5... Should I use only the command "recon-all -s OAS1_0074_MR1 -all", or I must add the option "-expert expert.opts" ?... In the first case freesurfer automatically use thresholds specified in expert.opts ?... Sincerely, Gonzalo Rojas Costa

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Re: [Freesurfer] Poor Intensity or Image Resolution?
by Bruce Fischl 02 Aug '11

02 Aug '11

Hi Antonella Are the sequence parameters the same? The way you convert should have no effect Bruce On Jul 27, 2011, at 11:51 AM, Antonella Kis <atorok9(a)yahoo.com> wrote: > Hi Bruce, > > I highly appreciate your great help/advice. > > Unfortunately, today I have another question: I finished running the recon-all for the new subjects for which I converted the dicom files in the NIFTI format as you advised me, using mri_convert. I was telling you that the .nii.gz file for this new subjects are very big , around 38 MB. Today I was analysing the volumes and I see there is a poor image in comparison with my other brains that were converted in a NIFTI format (having just 4 MB size) by someone else before me. > > My question is: is this poor image due to a different conversion way (I understood the other person used Mricron to convert the files) OR I need to do manually corrections adding control points for the intensity normalization. > > What is your suggestion/advise? > > Many thanks. > Antonella > > From: Bruce Fischl <fischl(a)nmr.mgh.harvard.edu> > To: Antonella Kis <atorok9(a)yahoo.com> > Cc: "freesurfer(a)nmr.mgh.harvard.edu" <freesurfer(a)nmr.mgh.harvard.edu> > Sent: Tuesday, July 26, 2011 5:53 PM > Subject: Re: [Freesurfer] Loading atlases > > Hi Antonella > > the atlas is not guaranteed to be correct. If it were we would just take the labels from it :) The only way to tell if it is correct is to look at the segmentations on top of the MR and see if they follow the visible boundary > > To get the surfaces you should do > > tkmedit SUBJECT1 brainmask.mgz lh.white \ > -aux T1.mgz -surfs \ > -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt > > cheers > Bruce > > > > On Tue, 26 Jul 2011, Antonella Kis wrote: > > > Hi, > > > > I would like to check if my subcortical segmentation is correct so I was running: > > > > tkmedit SUBJECT1 brainmask.mgz \ > > -aux T1.mgz -surfs \ > > -segmentation aseg.mgz $FREESURFER_HOME/FreeSurferColorLUT.txt > > > > 1). Pial (red line), and white (yellow line) surfaces are shown and I wonder how I can add a green lie for my orig surface? > > 2). After I load the aparc+aseg.mgz is theer a way to load and overlay the original/correct atlas so I can see if my segmentation is correct? > > > > Thank you very much. > > Antonella > > > > > > > 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. > > > <P27.tiff>

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xopts script...
by Gonzalo Rojas Costa 02 Aug '11

02 Aug '11

Hi: In the web page "FSTutorial/TroubleshootingData - Free Surfer Wiki" appears "Try using an xopts script first to change the intensity thresholds being used"... What is a xopts script ?... How can I use a xopts script to change the intensity thresholds ?... Sincerely, Gonzalo Rojas Costa

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