Re: [Freesurfer] Brain segmentation stats
It's because "Brain Segmentation Volume Without Ventricles" stat is computed with partial volume correction but "Number of Brain Segmentation Voxels" stat is not. Please refer to this wiki for more info. https://surfer.nmr.mgh.harvard.edu/fswiki/BrainVolume Sita On Wed, 1 Jul 2009, Jared Price wrote: Gurus, Looking over some stats recently I noticed that if you add up all of the freesurfer stats for ventricles, namely the left and right lateral ventricles plus 3rd, 4th, and 5th ventricles and subtract that from the "Number of Brain Segmentation Voxels" stat, you do not get the value of the "Brain Segmentation Volume Without Ventricles" stat. Anyone know why? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] monte-carlo simulation question
Dear Freesurfers, I ran a monte carlo simulation for thickness analyses using mri_glmfit and found new files in the contrast subdirectory. I was able to figure out what the first two represent, but was wondering if any one could clarify what information the rest of the files show: mc-z.negative.sig.cluster.summary : cluster summaries mc-z.negative.sig.ocn.annot : annotation of clusters mc-z.negative.sig.cluster.mgh : mc-z.negative.sig.ocn.mgh : mc-z.negative.sig.voxel.mgh : Thanks very much for your help, Prapti ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Brain segmentation stats
Gurus, Looking over some stats recently I noticed that if you add up all of the freesurfer stats for ventricles, namely the left and right lateral ventricles plus 3rd, 4th, and 5th ventricles and subtract that from the "Number of Brain Segmentation Voxels" stat, you do not get the value of the "Brain Segmentation Volume Without Ventricles" stat. Anyone know why? ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Freesurfer FSL Dimensions
Try mri_vol2vol --interp nearest --mov aparc+aseg.mgz --regheader --targ rawavg.mgz --o aparc+aseg.native.nii.gz Natalia Sanchez wrote: Hi: I am using Freesurfer and FSL together. My image dimensions initially are 256x256x128 in nii.gz format. I convert these images to .mgz using mri_convert and do cortical and subcoritcal segmentation in FreeSurfer. The outputs of the segmentation are the converted back into .nii.gz so I can use them in FSL, however, the dimensions of the Freesurfer outputs don't match with the FSL files. The freesurfer outputs are 256x256x256. Is there a way I can downsample this outputs to use them in FSL? Thanks! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] Freesurfer FSL Dimensions
Hi: I am using Freesurfer and FSL together. My image dimensions initially are 256x256x128 in nii.gz format. I convert these images to .mgz using mri_convert and do cortical and subcoritcal segmentation in FreeSurfer. The outputs of the segmentation are the converted back into .nii.gz so I can use them in FSL, however, the dimensions of the Freesurfer outputs don't match with the FSL files. The freesurfer outputs are 256x256x256. Is there a way I can downsample this outputs to use them in FSL? Thanks! ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_glmfit error
This can happen if the covariates have a very different scale (eg, age in years and something else in the range of 1-2). The product may have a different range as well. The product may be highly correlated with the first two CVs doug Susie Heo wrote: Hello, I am trying to run a cortical thickness analysis to look for an interaction between two continuous variables using mri_glmfit. I created an fsgd file including only the two original CVs to investigate main effects and obtained the output. When I added the interaction term (product of the two CVs) as a third continuous variable in my fsgd file and tried to run a dods analysis, I received the message: "ERROR: matrix is ill-conditioned or badly scaled." I don't understand how this could be the case. Is there a simple way to check whether my design matrix is ill-conditioned? Susie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Re: mkbrainmask not finding fslmaths
If you don't have FSL installed, then yes it will need to be. doug dah...@nmr.mgh.harvard.edu wrote: Perhaps I should have asked: Do I need to separately install FSL? Thanks Hi, I ran the following preproc-sess command and mkbrainmask-sess failed, with an error message of not finding fsmaths. I don't know where to be looking for this file and what previous command should have generated it. Can anyone help me out? Thanks! Dahlia. I ran: preproc-sess -sf sessid_subj31.txt -df sesspar -fwhm 5 The error message was: ERROR: cannot find either fslmaths for avwmaths ERROR: mkbrainmask failed ERROR: mkbrainmask-sess failed mkbrainmask-sess.log says: mkbrainmask-sess $Id: mkbrainmask-sess,v 1.12.2.1 2008/10/02 21:56:15 greve Exp $ Linux mbc.stanford.edu 2.6.22.9-61.fc6 #1 SMP Thu Sep 27 18:07:59 EDT 2007 x86_64 x86_64 x86_64 GNU/Linux Tue Jun 30 11:01:46 PDT 2009 /home/dahlia.sharon/functionals/fba_study_mtloc -maskstem brain -fsd bold -s mtloc_19may07 -d /home/dahlia.sharon/functionals/subj31 -update This is the command preproc-sess invoked: mkbrainmask -i 025/f.bhdr -o masks/brain.nii -thresh 0.1 -ndil 1 -nerode 0 The data is not on the network so I can't give paths. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] mri_glmfit error
Hello, I am trying to run a cortical thickness analysis to look for an interaction between two continuous variables using mri_glmfit. I created an fsgd file including only the two original CVs to investigate main effects and obtained the output. When I added the interaction term (product of the two CVs) as a third continuous variable in my fsgd file and tried to run a dods analysis, I received the message: "ERROR: matrix is ill-conditioned or badly scaled." I don't understand how this could be the case. Is there a simple way to check whether my design matrix is ill-conditioned? Susie ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] fsaverage across versions
Hi, my follow up question would be, how much has changed regarding fsaverage between freesurfer version 4.1.0 and 4.3.1? Is the added insula label the only change that has been made? Besides, when I load both annotations, the old and the new one, it seems to me almost every border of the parcellation has been shifted slightly. Is it how it's meant to be? I ask because I forgot to update the fsaverage in my separately stored Subjects_dir since version 4.1.0 and made a lot of analysis in the last months. To my mind it's good enough to rerun mri_surfcluster with the new fsaverage to get the updated annotations into my summary tables. Should that do the trick? Thanks again, Georg --- Iris, the registration targets were derived differently. With version 4, we automatically fill in all the ventricles. In verion 3, they were partially filled in manually. Version 3 creates a surface around the ventrical making it look like a sulcus, and this affects both the target and the registration to the target. So, on most of the surface, the registration will be very close, but it will deviate signifiacntly around the ventricles/medial wall. I think the fsfast in version 4 should work fine with the anatomicals (including fsaverage) of version 3. doug Steinmann, Iris wrote: Hi, we have several reconstructed brains, which were processed by freesurfer 3.0.5. We also kept using the fsaverage data from 3.0.5 in order to be consistent. We wish to do fMRI analysis with freesurfer/fs-fast 4.0.5 and found that talairach coordinates differ slightly when using the fsaverage from version 3.0.5 and the current fsaverage from 4.0.5. Yet, the both volumes appear pretty similar, the newer one maybe a little bit smoother. We would like to know what constitutes the exact difference between these two fsaverage datasets and whether it is possible to use the new version for analysis with the "old" fsaverage data without getting inconsistent results. Thanks a lot, Iris ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center [EMAIL PROTECTED] Phone Number: 617-724-2358 Fax: 617-726-7422 In order to help us help you, please follow the steps in: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] standardize in asegstata2table
Can I have the volumes in the standardize space? Thanks, anita 2009/7/1 Bruce Fischl > Hi Anita, > > no, they are in native space. > > cheers, > Bruce > > On Wed, 1 Jul 2009, Anita di Iasio wrote: > > Hi all, >> I have a question. >> In the table created from asegstats2table, are the volumes standardized to >> Talairach space? >> or are they in their orig space? >> thank in advanced, >> anita >> ___ >> Freesurfer mailing list >> Freesurfer@nmr.mgh.harvard.edu >> https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer >> >> >> >> ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] FreeSurfer: extracting regions from segmentation
Hi Judit, the fornix is labeled in the aseg, not the parcellation, although this is not the default). If you rerun mri_cc with the -fornix option it will write a volume named mri/fornix.mgz with the fornix in it. cheers, Bruce On Wed, 1 Jul 2009, Judit Haasz wrote: Hi, We are trying to extract certain regions from FreeSurfer segmentation. There are couple of regions which are not found in the output files. We are currently searching for the regions in 13 output files. The regions are the following: right fornix (508), left fornix (558), right PLIC (158), left PLIC (157) and the starting, way and end points for cingulum and CST. Could you let us know in which file would we be able to find these regions? Is it possible that some regions are empty? Thank you for your help Judit Haasz ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] FreeSurfer: extracting regions from segmentation
Hi, We are trying to extract certain regions from FreeSurfer segmentation. There are couple of regions which are not found in the output files. We are currently searching for the regions in 13 output files. The regions are the following: right fornix (508), left fornix (558), right PLIC (158), left PLIC (157) and the starting, way and end points for cingulum and CST. Could you let us know in which file would we be able to find these regions? Is it possible that some regions are empty? Thank you for your help Judit Haasz ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] standardize in asegstata2table
Hi Anita, no, they are in native space. cheers, Bruce On Wed, 1 Jul 2009, Anita di Iasio wrote: Hi all, I have a question. In the table created from asegstats2table, are the volumes standardized to Talairach space? or are they in their orig space? thank in advanced, anita ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] Cannot allocate memory / can't allocate region
Hi Juergen, how much ram do you have in the machine? Bruce On Wed, 1 Jul 2009, Jürgen Hänggi wrote: Dear FS experts I am using high resolution (0.75x0.75x0.75 mm) data within FS but the following error occurred: ... vertex spacing 0.69 +- 0.21 (0.00-->6.06) (max @ vno 265258 --> 114262) face area 0.19 +- 0.10 (0.00-->4.49) mris_make_surfaces(49536) malloc: *** mmap(size=1355776) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(937, 361, 612): could not allocate 1353028 bytes for 356th slice 000: dt: 0., sse=4822516.5, rms=2.25 rms = 2.94, time step reduction 1 of 3 to 0.250... 043: dt: 0.2500, sse=4898456.5, rms=1.89 rms = 1.86, time step reduction 2 of 3 to 0.125... 044: dt: 0.2500, sse=5293477.5, rms=1.86 045: dt: 0.1250, sse=5277681.5, rms=1.76 046: dt: 0.1250, sse=5237215.5, rms=1.70 rms = 1.69, time step reduction 3 of 3 to 0.062... 047: dt: 0.1250, sse=5270459.0, rms=1.69 positioning took 16.1 minutes inhibiting deformation at non-cortical midline structures... correcting aseg with surfaces... Cannot allocate memory Darwin juergen-haenggis-mac-pro.local 9.7.0 Darwin Kernel Version 9.7.0: Tue Mar 31 22:52:17 PDT 2009; root:xnu-1228.12.14~1/RELEASE_I386 i386 recon-all exited with ERRORS at Wed Jul 1 04:20:34 CEST 2009 [juergen-haenggis-mac-pro:subjects/roman_p_highres_div100/mri] I am using FS 4.4, Mac OSX 10.5, 8 GB RAM, memoryuse unlimited, descriptors 8192 The process terminated before all RAM is active and no swap is used. Any idea? Thanks in advance Regards Jürgen Juergen Haenggi Ph.D. (Dr. des.) Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
RES: [Freesurfer] Cannot allocate memory / can't allocate region
Check ulimit -m That's the max mem per process. ulimit -m 0 Maybe will help. -- Pedro Paulo Jr E71 Nokia -Msg original- De: Jürgen Hänggi Enviada: 01/07/2009 02:36:36 Para: Freesurfer Mailinglist Assunto: [Freesurfer] Cannot allocate memory / can't allocate region Dear FS experts I am using high resolution (0.75x0.75x0.75 mm) data within FS but the following error occurred: ... vertex spacing 0.69 +- 0.21 (0.00-->6.06) (max @ vno 265258 --> 114262) face area 0.19 +- 0.10 (0.00-->4.49) mris_make_surfaces(49536) malloc: *** mmap(size=1355776) failed (error code=12) *** error: can't allocate region *** set a breakpoint in malloc_error_break to debug MRIalloc(937, 361, 612): could not allocate 1353028 bytes for 356th slice 000: dt: 0., sse=4822516.5, rms=2.25 rms = 2.94, time step reduction 1 of 3 to 0.250... 043: dt: 0.2500, sse=4898456.5, rms=1.89 rms = 1.86, time step reduction 2 of 3 to 0.125... 044: dt: 0.2500, sse=5293477.5, rms=1.86 045: dt: 0.1250, sse=5277681.5, rms=1.76 046: dt: 0.1250, sse=5237215.5, rms=1.70 rms = 1.69, time step reduction 3 of 3 to 0.062... 047: dt: 0.1250, sse=5270459.0, rms=1.69 positioning took 16.1 minutes inhibiting deformation at non-cortical midline structures... correcting aseg with surfaces... Cannot allocate memory Darwin juergen-haenggis-mac-pro.local 9.7.0 Darwin Kernel Version 9.7.0: Tue Mar 31 22:52:17 PDT 2009; root:xnu-1228.12.14~1/RELEASE_I386 i386 recon-all exited with ERRORS at Wed Jul 1 04:20:34 CEST 2009 [juergen-haenggis-mac-pro:subjects/roman_p_highres_div100/mri] I am using FS 4.4, Mac OSX 10.5, 8 GB RAM, memoryuse unlimited, descriptors 8192 The process terminated before all RAM is active and no swap is used. Any idea? Thanks in advance Regards Jürgen Juergen Haenggi Ph.D. (Dr. des.) Division Neuropsychology Institute of Psychology University of Zurich Binzmuehlestrasse 14, PO Box 25 8050 Zurich, Switzerland 0041 44 635 73 97 (phone office) 0041 76 445 86 84 (phone mobile) 0041 44 635 74 09 (fax office) BIN 4.D.04 (office room number) j.haenggi[at]psychologie.uzh.ch (email) http://www.psychologie.uzh.ch/neuropsy/ (website) http://www.juergenhaenggi.ch (private website) This e-mail (and any attachment/s) contains confidential and/or privileged information. If you are not the intended recipient (or have received this e-mail in error) please notify the sender immediately and destroy this e-mail. Any unauthorised copying, disclosure or distribution of the material in this e-mail is strictly forbidden. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] standardize in asegstata2table
Hi all, I have a question. In the table created from asegstats2table, are the volumes standardized to Talairach space? or are they in their orig space? thank in advanced, anita ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
