Re: [Freesurfer] dwi_motion Tracula
Hi Cat - I'll have to see your trac-all.log, I can't tell what is going on just from that one line. a.y On Tue, 22 Jul 2014, Cat Chong wrote: Dear Anastasia, With the new Tracula update installed, I ran the command: trac-all –qa –c dmrirc_file with location of bval specified and received the following error after ‘Loading volume-to-baseline affine transformations’ Could not open ../dmri/ dwi.ecclog for reading. It seems like all subjects do have the dwi.ecclog in their /dmri/ directories. Any ideas of what might have gone wrong? Cheers, Cat On Monday, July 21, 2014 1:53 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Cat - Just install the update and run trac-all -qa. This will produce the motion measures. Check the tutorial for where to find the output. a.y On Mon, 21 Jul 2014, Cat Chong wrote: Hello Anastasia, I ran Tracula on Freesurfer 5.3 but without the 2013 Tracula updates. Now, I would like to use the command dwi_motion on my data. I have installed the updates, but will I have to completely reprocess my data inducing steps trac-all -prep, trace-all -bedp, and trac-all path in order to use dwi_motion? cheers, Cat ___ Freesurfer mailing list 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. ___ Freesurfer mailing list 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.
Re: [Freesurfer] Looking at dtifit_V1 in freeview
Hi Emily - Actually, there is a bug in the 5.3 version of freeview in that specific feature. But you can use fslview - you select the V1 file, click on the (i) button and choose Display as: Lines. a.y On Tue, 22 Jul 2014, ebell...@uwm.edu wrote: Hi all, I was wondering how you go about looking at dtifit_V1 (the primary eigenvector of the tensors) displayed as lines in freeview? Emily ___ 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 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.
Re: [Freesurfer] Pathstat.byvoxel.txt question
Hi Sarina - It's linear interpolation. a.y On Wed, 23 Jul 2014, Sarina Sacco wrote: Hi all freesurfer experts , I have a question about the command trac-all-stat-c ,what is the interpolation that uses? ___ Freesurfer mailing list 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.
[Freesurfer] Diffusion analysis qs
Dear Anastasia Michael, Thank u for your answers (I attached my last email and your answers at the end of this email. I still want to specify my question. If I only want to extract FA values using the following script (see script below), and I know that an angle was applied during the dMRI scans, should I use the rotated gradient matrix ? When I first analyzed 20 subjects with the gradient matrix that is published for a T3 Philips magnet (I also read the gradients from the dicom header - they were the same) I got reasonable results - but now I don't know what to think of them... __ source ~/Desktop/fs_script dt_recon --i /usr/local/freesurfer/subjects/Anatomy0207/DTI/I160.dcm --s Anatomy0207 --o /usr/local/freesurfer/subjects/Anatomy0207/DTI --b /usr/local/freesurfer/subjects/Anatomy0207/DTI/bvals.bval /usr/local/freesurfer/subjects/Anatomy0207/DTI/bvecs.bvec To check results, run: tkregister2 --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/lowb.nii --reg /usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat --surf tkregister2 --s fsaverage --surf white --reg /usr/local/freesurfer/subjects/Anatomy0207/DTI/mask-tal.nii.reg --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/mask-tal.nii tkregister2 --s fsaverage --surf white --reg /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-tal.nii.reg --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-tal.nii freeview -v /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii /usr/local/freesurfer/subjects/Anatomy0207/DTI/adc.nii freeview -v /usr/local/freesurfer/subjects/Anatomy0207/mri/brain.mgz /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii:reg=register.dat:colormap=heat:heatscale=.2,.2,1 tkmedit Anatomy0207 orig.mgz -aux brain.mgz -seg wmparc.mgz -reg /usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat -overlay /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii -fthresh 0.2 -fmax 1 mri_vol2vol --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/lowb.nii \ --targ /usr/local/freesurfer/subjects/Anatomy0207/mri/wmparc.mgz \ --inv --interp nearest --o /usr/local/freesurfer/subjects/Anatomy0207/mri/wmparc2diff.mgz \ --reg /usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat --no-save-reg mri_vol2vol --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/lowb.nii \ --targ /usr/local/freesurfer/subjects/Anatomy0207/mri/aparc+aseg.mgz \ --inv --interp nearest --o /usr/local/freesurfer/subjects/Anatomy0207/mri/aparc+aseg2diff.mgz \ --reg /usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat --no-save-reg freeview -v /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii \ /usr/local/freesurfer/subjects/Anatomy0207/mri/aparc+aseg2diff.mgz:colormap=lut mri_mask /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii \ /usr/local/freesurfer/subjects/Anatomy0207/mri/wmparc2diff.mgz \ /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-masked.mgz freeview -v /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-masked.mgz /usr/local/freesurfer/subjects/Anatomy0207/mri/aparc+aseg2diff.mgz:colormap=lut mri_segstats --seg /usr/local/freesurfer/subjects/Anatomy0207/mri/wmparc2diff.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-masked.mgz --sum /usr/local/freesurfer/subjects/Anatomy0207/stats/all_stats_fa-masked __ It'd be nice if things were that simple, but! Although the pre-processing is done with FSL tools, tractography is done with locally written code. Some gradient sets may appear to work with FSL, but they won't work for us. For example, some dicom converters may perform a L-R flip as preparation for feeding the gradient vectors into FSL. We need the unflipped vectors because, instead of flipping vectors, we convert both vectors and images to LAS orientation. This ensures that they work both for FSL and for us, and that you can view things correctly in both freeview and fslview, without the subject looking like it's hanging upside down from its bat cave or some such awkward arrangement. In the end, the best way of knowing that the gradient table is correct is to run one example subject through and view the eigenvectors of the tensors as lines to see if they're pointing in the right direction. (Even though the tensors themselves aren't used for tractography, they're good for troubleshooting.) On Mon, 21 Jul 2014, Harms, Michael wrote: FS uses FSL tools under the hood, so you want to use the bvecs that are rotated into the axes of the scan. cheers, -MH --? Michael Harms, Ph.D. --- Conte Center for the Neuroscience of Mental Disorders Washington University School of Medicine Department of Psychiatry, Box 8134
Re: [Freesurfer] Diffusion analysis qs
Hi Rotem - The FA values are actually invariant to a rotation of the gradient vectors. You can test that yourself. If, however, you get different FA maps with the different gradient tables, then something else is going on and not a simple rotation. a.y On Wed, 23 Jul 2014, Rotem Saar wrote: Dear Anastasia Michael, Thank u for your answers (I attached my last email and your answers at the end of this email. I still want to specify my question. If I only want to extract FA values using the following script (see script below), and I know that an angle was applied during the dMRI scans, should I use the rotated gradient matrix ? When I first analyzed 20 subjects with the gradient matrix that is published for a T3 Philips magnet (I also read the gradients from the dicom header - they were the same) I got reasonable results - but now I don't know what to think of them... ___ ___ source ~/Desktop/fs_script dt_recon --i /usr/local/freesurfer/subjects/Anatomy0207/DTI/I160.dcm --s Anatomy0207 --o /usr/local/freesurfer/subjects/Anatomy0207/DTI --b /usr/local/freesurfer/subjects/Anatomy0207/DTI/bvals.bval /usr/local/freesurfer/subjects/Anatomy0207/DTI/bvecs.bvec To check results, run: tkregister2 --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/lowb.nii --reg /usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat --surf tkregister2 --s fsaverage --surf white --reg /usr/local/freesurfer/subjects/Anatomy0207/DTI/mask-tal.nii.reg --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/mask-tal.nii tkregister2 --s fsaverage --surf white --reg /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-tal.nii.reg --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-tal.nii freeview -v /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii /usr/local/freesurfer/subjects/Anatomy0207/DTI/adc.nii freeview -v /usr/local/freesurfer/subjects/Anatomy0207/mri/brain.mgz/usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii:reg=register.dat:colo rmap=heat:heatscale=.2,.2,1 tkmedit Anatomy0207 orig.mgz -aux brain.mgz -seg wmparc.mgz -reg /usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat -overlay /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii -fthresh 0.2 -fmax 1 mri_vol2vol --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/lowb.nii \ --targ /usr/local/freesurfer/subjects/Anatomy0207/mri/wmparc.mgz \ --inv --interp nearest --o /usr/local/freesurfer/subjects/Anatomy0207/mri/wmparc2diff.mgz \ --reg /usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat --no-save-reg mri_vol2vol --mov /usr/local/freesurfer/subjects/Anatomy0207/DTI/lowb.nii \ --targ /usr/local/freesurfer/subjects/Anatomy0207/mri/aparc+aseg.mgz \ --inv --interp nearest --o /usr/local/freesurfer/subjects/Anatomy0207/mri/aparc+aseg2diff.mgz \ --reg /usr/local/freesurfer/subjects/Anatomy0207/DTI/register.dat --no-save-reg freeview -v /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii \ /usr/local/freesurfer/subjects/Anatomy0207/mri/aparc+aseg2diff.mgz:colormap =lut mri_mask /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa.nii \ /usr/local/freesurfer/subjects/Anatomy0207/mri/wmparc2diff.mgz \ /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-masked.mgz freeview -v /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-masked.mgz/usr/local/freesurfer/subjects/Anatomy0207/mri/aparc+aseg2diff.mgz:colormap =lut mri_segstats --seg /usr/local/freesurfer/subjects/Anatomy0207/mri/wmparc2diff.mgz --ctab $FREESURFER_HOME/FreeSurferColorLUT.txt --i /usr/local/freesurfer/subjects/Anatomy0207/DTI/fa-masked.mgz --sum /usr/local/freesurfer/subjects/Anatomy0207/stats/all_stats_fa-masked ___ ___ It'd be nice if things were that simple, but! Although the pre-processing is done with FSL tools, tractography is done with locally written code. Some gradient sets may appear to work with FSL, but they won't work for us. For example, some dicom converters may perform a L-R flip as preparation for feeding the gradient vectors into FSL. We need the unflipped vectors because, instead of flipping vectors, we convert both vectors and images to LAS orientation. This ensures that they work both for FSL and for us, and that you can view things correctly in both freeview and fslview, without the subject looking like it's hanging upside down from its bat cave or some such awkward arrangement. In the end, the best way of knowing that the gradient table is correct is to run one example subject through and view the eigenvectors of the tensors as lines to see if they're pointing in the right direction. (Even though the tensors themselves aren't used for tractography, they're good for troubleshooting.) On Mon, 21 Jul 2014, Harms, Michael wrote: FS uses FSL tools under the
Re: [Freesurfer] Pathstat.byvoxel.txt question
Thank you for help. Il 23/lug/2014 10:19 Anastasia Yendiki ayend...@nmr.mgh.harvard.edu ha scritto: Hi Sarina - It's linear interpolation. a.y On Wed, 23 Jul 2014, Sarina Sacco wrote: Hi all freesurfer experts , I have a question about the command trac-all-stat-c ,what is the interpolation that uses? ___ Freesurfer mailing list 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. ___ Freesurfer mailing list 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.
[Freesurfer] running freesurfer subcortical segmentation on a T2 weighted image only ?
Dear all, I was wondering if there is a way to use the segmentation of freesurfer on a T2 weighted image only (without a T1 weighted image). Sincerely Vincent Noblet ___ Freesurfer mailing list 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.
Re: [Freesurfer] bad freesurfer segmentation
Just for the record, I accidentally e-mailed you that the slice thickness was 2 mm, I now found out that the slice thickness is just 1 mm. Doety ___ Freesurfer mailing list 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.
Re: [Freesurfer] lgi for longitudinal scans
hi Martin, I just tried this and it resulted in errors/ Do I not have to specify a flag for the baseid or for each subject, eg -s? What I did (according to your suggestion) recon-all -long XXX_1.long XXX_2.long -localGI This did not work? Do you know why potentially? On Wed, Mar 26, 2014 at 3:28 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Anna, no, you would still do: recon-all -long tpid baseid -localGI just not use the '-all'. Best, Martin On 03/26/2014 11:12 AM, Anna Jonsson wrote: thank you. But if the lnog process has already been done and these induviduals already have long directories so to speak, I would just put the lgi flag on as normal but just replace the subject name with the long subject name eg ? recon-all -s _long -localGI Thank you On Sat, Mar 15, 2014 at 2:07 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Anna, for the image processing, you just add the lgi flag to the regular longitudinal recon-all command recon-all -long …… -lgi for the analysis after that you use the long directories. Best, Martin On Mar 15, 2014, at 10:04 AM, Anna Jonsson ajonsso...@gmail.com wrote: Dear group, If I want conduct gyrification analyses on the long runs that have been through the longitudinal stream, do I just perform the normal baseline command on the .long data? thank you, kind wishes Anna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer - Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ Freesurfer mailing list 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. -- Martin Reuter, Ph.D. Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ Freesurfer mailing list 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.
Re: [Freesurfer] running freesurfer subcortical segmentation on a T2 weighted image only ?
Hi Vincent you mean to create it from a T2? Not really in our distributed version, although Koen Van Leemput (ccd) has some tools that can do this I believe. cheers Bruce On Wed, 23 Jul 2014, Vincent Noblet wrote: Dear all, I was wondering if there is a way to use the segmentation of freesurfer on a T2 weighted image only (without a T1 weighted image). Sincerely Vincent Noblet ___ 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 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.
Re: [Freesurfer] recon-all error
Hi Cheng do the cross-sectional runs look okay? The base? If so, does the first intensity normalized images look ok (the T1.mgz and the nu.mgz)? If you can't track it down, upload the subject and we will take a look cheers Bruce On Wed, 23 Jul 2014, Cheng Peng wrote: Hi, Freesurfer experts: I encountered an error message while i was attempting to run a longitudinal study (following the instructions from https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing, step 2 under workflow summary) egister_mri: find_optimal_transform find_optimal_transform: nsamples 2185, passno 0, spacing 8 GCAhistoScaleImageIntensities: could not find wm peak resetting wm mean[0]: 102 -- 107 resetting gm mean[0]: 64 -- 64 input volume #1 is the most T1-like using real data threshold=0.0 skull bounding box = (0, 0, 0) -- (255, 255, 255) using (85, 85, 128) as brain centroid... mean wm in atlas = 107, using box (53,53,96) -- (116, 116,159) to find MRI wm WARNING: gca.c::GCAhistoScaleImageIntensities: h_mri-nbins=1, mri_peak=-1 before smoothing, mri peak at 0 WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri-nbins=1, mri_peak=-1 after smoothing, mri peak at 0, scaling input intensities by inf It appears that the skull strip step has failed as brainmask.mgz is completely blank. I tried to look up the error message online but found little help there. I would really appreciate it if someone can explain the problem or where to look for an explaination. I attached the recon-all error log with this email, i would also include nu.mgz but the last email attached with that was blocked due to the size of the image. Thanks! Best Regards, Cheng Peng Maryland Neuroimaging Center ___ Freesurfer mailing list 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.
Re: [Freesurfer] Converting volume to label
Hi all, We are still struggling with this issue - any ideas? Here is some more information: - The surface that we are trying to label is the subject colin, as found here: http://mindboggle.info/data.html. We get two errors when loading in tksurfer (1) surfer: Tailairach xform file not found (ignored) (2) MRISreadVertexPosition(/Applications/.../subject/colin/surf/lh.org); No such file or directory However, the surface does load and can be manipulated (a label can be created manually and filled in). - We first tried to create a surface to overlay from our .nii file (which does load in Freeview) with mri_vol2surf. Our .nii had been converted to a .mgz with a corresponding .dat file using [COMMAND]. We tried --out_type paint (with file type .w) and --out_type mgh (with file type .mgh), but both gave the same error: MRISread: file '.../surf/test-lh.w' has 0 vertices! Probably trying to use a scalar data file as a surface! - We next tried mri_cor2label --i cluster1_roi.nii --l ./cluster1.label --id 1. In Freeview with our .nii file loaded, we verified that our volume of interest does have a value of 1, and unselected regions have a value of 0. It seems to run properly, finding unassigned vertices in label and assigning vertex numbers to label. However, in tksurfer, when we select File Load label value file cluster1.label, we get the following error: sclv_load_label_value_file: error reading line 1: 9389 We have two main questions - any advice would be greatly appreciated! (1) From my understanding of label files, the first line should be the number of vertices in the label file. Why then do we get an error in reading this line when loading the label file? (2) Are the initial errors pertaining to a lack of files for our template surface going to create a problem when we do successfully load our label file? If so, is there a way to align the two in the same coordinate space? Thank you! -- Sarah Weiss From: Weiss, Sarah Sent: Friday, July 18, 2014 3:02 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Converting volume to label Dear Freesurfer experts, We are trying to convert a volume created in SPM and saved as a .nii file into a label to overlay on a Freesurfer surface. We are using a template surface found online, colin (http://mindboggle.info/data.html). We are able to display our .nii in freeview successfully. The voxels that we wish to label have a value of 1, and elsewhere in the file the value is 0. The command that we are running is: mri_cor2label --i cluster3_roi.nii --l ./cluster3_roi.label --id 1 We do get a series of points as output. However, when we load the consequent label, it doesn't display correctly - the points are discontinuous, and don't correspond to the correct parts of the brain. Here are some of the error messages that we get: ltMNIreadEx: could not open file /Applications/freesurfer/subjects/rk/mri/transforms/talairach.xfm No such file or directory MRISreadVertexPosition(/Applications/freesurfer/subjects/rk/surf/rh.orig): could not open file /Applications/freesurfer/subjects/rk/surf/rh.orig No such file or directory MRISreadOriginalProperties: could not read surface file /Applications/freesurfer/subjects/rk/surf/rh.orig No such file or directory 0 nonzero vertices found label stat field identically zero - setting to 1 9389 unassigned vertices in label - building spatial LUT... assigning vertex numbers to label... Why does it say that 0 nonzero vertices have been found, yet it selects 9389 vertices? Is there an additional option that we should be utilizing? Is a label the correct way to create what we are looking for, or would an overlay be more appropriate? If the latter is the case, should we be using mri_vol2surf? Thank you in advance for your assistance! Best, Sarah Weiss and Robert Kim ___ Freesurfer mailing list 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.
Re: [Freesurfer] Converting volume to label
Hi Sarah Doug is out of email contact for another week or so, and this might have to wait for his return. In the meantime: are you trying to overlay it on the colin surface or on some other subject (rk?). If you load the [lr]h.white surface over the volume for colin does it look ok? cheers Bruce On Wed, 23 Jul 2014, Weiss, Sarah wrote: Hi all, We are still struggling with this issue - any ideas? Here is some more information: - The surface that we are trying to label is the subject colin, as found here: http://mindboggle.info/data.html. We get two errors when loading in tksurfer (1) surfer: Tailairach xform file not found (ignored) (2) MRISreadVertexPosition(/Applications/.../subject/colin/surf/lh.org); No such file or directory However, the surface does load and can be manipulated (a label can be created manually and filled in). - We first tried to create a surface to overlay from our .nii file (which does load in Freeview) with mri_vol2surf. Our .nii had been converted to a .mgz with a corresponding .dat file using [COMMAND]. We tried --out_type paint (with file type .w) and --out_type mgh (with file type .mgh), but both gave the same error: MRISread: file '.../surf/test-lh.w' has 0 vertices! Probably trying to use a scalar data file as a surface! - We next tried mri_cor2label --i cluster1_roi.nii --l ./cluster1.label --id 1. In Freeview with our .nii file loaded, we verified that our volume of interest does have a value of 1, and unselected regions have a value of 0. It seems to run properly, finding unassigned vertices in label and assigning vertex numbers to label. However, in tksurfer, when we select File Load label value file cluster1.label, we get the following error: sclv_load_label_value_file: error reading line 1: 9389 We have two main questions - any advice would be greatly appreciated! (1) From my understanding of label files, the first line should be the number of vertices in the label file. Why then do we get an error in reading this line when loading the label file? (2) Are the initial errors pertaining to a lack of files for our template surface going to create a problem when we do successfully load our label file? If so, is there a way to align the two in the same coordinate space? Thank you! -- Sarah Weiss From: Weiss, Sarah Sent: Friday, July 18, 2014 3:02 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Converting volume to label Dear Freesurfer experts, We are trying to convert a volume created in SPM and saved as a .nii file into a label to overlay on a Freesurfer surface. We are using a template surface found online, colin (http://mindboggle.info/data.html). We are able to display our .nii in freeview successfully. The voxels that we wish to label have a value of 1, and elsewhere in the file the value is 0. The command that we are running is: mri_cor2label --i cluster3_roi.nii --l ./cluster3_roi.label --id 1 We do get a series of points as output. However, when we load the consequent label, it doesn't display correctly - the points are discontinuous, and don't correspond to the correct parts of the brain. Here are some of the error messages that we get: ltMNIreadEx: could not open file /Applications/freesurfer/subjects/rk/mri/transforms/talairach.xfm No such file or directory MRISreadVertexPosition(/Applications/freesurfer/subjects/rk/surf/rh.orig): could not open file /Applications/freesurfer/subjects/rk/surf/rh.orig No such file or directory MRISreadOriginalProperties: could not read surface file /Applications/freesurfer/subjects/rk/surf/rh.orig No such file or directory 0 nonzero vertices found label stat field identically zero - setting to 1 9389 unassigned vertices in label - building spatial LUT... assigning vertex numbers to label... Why does it say that 0 nonzero vertices have been found, yet it selects 9389 vertices? Is there an additional option that we should be utilizing? Is a label the correct way to create what we are looking for, or would an overlay be more appropriate? If the latter is the case, should we be using mri_vol2surf? Thank you in advance for your assistance! Best, Sarah Weiss and Robert Kim ___ Freesurfer mailing list 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.
Re: [Freesurfer] lgi for longitudinal scans
Hi Anna, that was not my suggestion, I suggested to pass both the cross sectional time point ID and the base id (together with the long flag) and additionally the -localGI flag. So if you time point 1 is XXX_1 and time point 2 is XXX_2 and your base is XXX_base then recon-all -long XXX_1 XXX_base -localGI and for the second time point recon-all -long XXX_2 XXX_base -localGI The base is not one of your time points, it gets created in the -base step and you give it a name (here XXX_base). In order for the above to work you need 5 directories per subject: the 2 cross XXX_1 and XXX_2 the base XXX_base the results of the -long runs: XXX_1.long.XXX_base XXX_2.long.XXX_base the last two are the ones where the GI will be created. Best, Martin On Jul 23, 2014, at 9:02 AM, Anna Jonsson ajonsso...@gmail.com wrote: hi Martin, I just tried this and it resulted in errors/ Do I not have to specify a flag for the baseid or for each subject, eg -s? What I did (according to your suggestion) recon-all -long XXX_1.long XXX_2.long -localGI This did not work? Do you know why potentially? On Wed, Mar 26, 2014 at 3:28 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Anna, no, you would still do: recon-all -long tpid baseid -localGI just not use the '-all'. Best, Martin On 03/26/2014 11:12 AM, Anna Jonsson wrote: thank you. But if the lnog process has already been done and these induviduals already have long directories so to speak, I would just put the lgi flag on as normal but just replace the subject name with the long subject name eg ? recon-all -s _long -localGI Thank you On Sat, Mar 15, 2014 at 2:07 PM, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote: Hi Anna, for the image processing, you just add the lgi flag to the regular longitudinal recon-all command recon-all -long …… -lgi for the analysis after that you use the long directories. Best, Martin On Mar 15, 2014, at 10:04 AM, Anna Jonsson ajonsso...@gmail.com wrote: Dear group, If I want conduct gyrification analyses on the long runs that have been through the longitudinal stream, do I just perform the normal baseline command on the .long data? thank you, kind wishes Anna ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer - Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ Freesurfer mailing list 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. -- Martin Reuter, Ph.D. Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu - Dr. Martin Reuter Assistant in Neuroscience - Massachusetts General Hospital Instructor in Neurology - Harvard Medical School MGH / HMS / MIT A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ Freesurfer mailing list 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
Re: [Freesurfer] recon-all error
Hi, Bruce: I attached the file with an email and sent it to you an hour ago and received an automatic reply saying it's pending for approval due to the size of the email. Is there another way to upload my image or it's getting processed? I don't want to spam you guys since i already sent it twice and got the same result. Thanks! Cheng Peng On Wednesday, July 23, 2014 9:39 AM, Cheng Peng pcdula...@yahoo.com wrote: Hi, Bruce, I attached the nu.mgz file with this email, i'm at home right now and would upload T1.mgz later if need to. As far as i know individual recon-all runs were completed without error (two scans on one subject, two hours apart), really appreciate the help! Cheng Peng Maryland Neuroimaging Center On Wednesday, July 23, 2014 9:32 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Cheng do the cross-sectional runs look okay? The base? If so, does the first intensity normalized images look ok (the T1.mgz and the nu.mgz)? If you can't track it down, upload the subject and we will take a look cheers Bruce On Wed, 23 Jul 2014, Cheng Peng wrote: Hi, Freesurfer experts: I encountered an error message while i was attempting to run a longitudinal study (following the instructions from https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing, step 2 under workflow summary) egister_mri: find_optimal_transform find_optimal_transform: nsamples 2185, passno 0, spacing 8 GCAhistoScaleImageIntensities: could not find wm peak resetting wm mean[0]: 102 -- 107 resetting gm mean[0]: 64 -- 64 input volume #1 is the most T1-like using real data threshold=0.0 skull bounding box = (0, 0, 0) -- (255, 255, 255) using (85, 85, 128) as brain centroid... mean wm in atlas = 107, using box (53,53,96) -- (116, 116,159) to find MRI wm WARNING: gca.c::GCAhistoScaleImageIntensities: h_mri-nbins=1, mri_peak=-1 before smoothing, mri peak at 0 WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri-nbins=1, mri_peak=-1 after smoothing, mri peak at 0, scaling input intensities by inf It appears that the skull strip step has failed as brainmask.mgz is completely blank. I tried to look up the error message online but found little help there. I would really appreciate it if someone can explain the problem or where to look for an explaination. I attached the recon-all error log with this email, i would also include nu.mgz but the last email attached with that was blocked due to the size of the image. Thanks! Best Regards, Cheng Peng Maryland Neuroimaging Center ___ Freesurfer mailing list 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.___ Freesurfer mailing list 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.
Re: [Freesurfer] recon-all error
Hi Cheng if you go to our wiki there are instructions for uploading big datasets using either ftp or our filedrop cheers Bruce On Wed, 23 Jul 2014, Cheng Peng wrote: Hi, Bruce: I attached the file with an email and sent it to you an hour ago and received an automatic reply saying it's pending for approval due to the size of the email. Is there another way to upload my image or it's getting processed? I don't want to spam you guys since i already sent it twice and got the same result. Thanks! Cheng Peng On Wednesday, July 23, 2014 9:39 AM, Cheng Peng pcdula...@yahoo.com wrote: Hi, Bruce, I attached the nu.mgz file with this email, i'm at home right now and would upload T1.mgz later if need to. As far as i know individual recon-all runs were completed without error (two scans on one subject, two hours apart), really appreciate the help! Cheng Peng Maryland Neuroimaging Center On Wednesday, July 23, 2014 9:32 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Cheng do the cross-sectional runs look okay? The base? If so, does the first intensity normalized images look ok (the T1.mgz and the nu.mgz)? If you can't track it down, upload the subject and we will take a look cheers Bruce On Wed, 23 Jul 2014, Cheng Peng wrote: Hi, Freesurfer experts: I encountered an error message while i was attempting to run a longitudinal study (following the instructions from https://surfer.nmr.mgh.harvard.edu/fswiki/LongitudinalProcessing, step 2 under workflow summary) egister_mri: find_optimal_transform find_optimal_transform: nsamples 2185, passno 0, spacing 8 GCAhistoScaleImageIntensities: could not find wm peak resetting wm mean[0]: 102 -- 107 resetting gm mean[0]: 64 -- 64 input volume #1 is the most T1-like using real data threshold=0.0 skull bounding box = (0, 0, 0) -- (255, 255, 255) using (85, 85, 128) as brain centroid... mean wm in atlas = 107, using box (53,53,96) -- (116, 116,159) to find MRI wm WARNING: gca.c::GCAhistoScaleImageIntensities: h_mri-nbins=1, mri_peak=-1 before smoothing, mri peak at 0 WARNING2: gca.c::GCAhistoScaleImageIntensities: h_mri-nbins=1, mri_peak=-1 after smoothing, mri peak at 0, scaling input intensities by inf It appears that the skull strip step has failed as brainmask.mgz is completely blank. I tried to look up the error message online but found little help there. I would really appreciate it if someone can explain the problem or where to look for an explaination. I attached the recon-all error log with this email, i would also include nu.mgz but the last email attached with that was blocked due to the size of the image. Thanks! Best Regards, Cheng Peng Maryland Neuroimaging Center ___ Freesurfer mailing list 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] qcache number of vertices error
Hello, I am running into an error when using qcache. Subjects that have had manual edits are exited with errors, while subjects that have not had edits run fine. All subjects have had –make all ran after edits and finished without errors. I have read about this problem and tried some of the solutions but am still getting errors. When I first tried running –qcache I received this error: Reading curvature file /scratch/lfs/aoshea/testAndrew/processedSubjects/1492/surf/lh.volume ERROR: number of vertices in /scratch/lfs/aoshea/testAndrew/processedSubjects/1492/surf/lh.volume does not match surface (128222,130849) ERROR: reading curvature file Linux c2a-s21.ufhpc 2.6.32-358.23.2.el6.x86_64 #1 SMP Sat Sep 14 05:32:37 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 1492 exited with ERRORS at Wed Jul 23 10:32:24 EDT 2014 To make sure everything was ran I re-ran –make all and got make: Nothing to be done for `all’. I then ran –vno_match_check and it said everything was fine: Pass: all surfaces and surface data for subject 1492 for hemi lh have the same number of vertices. Pass: all surfaces and surface data for subject 1492 for hemi rh have the same number of vertices. I saw Doug gave this suggestion ( using –surf volume –qcache) to someone who was having the same problem this resulted in qcache getting past the volume stage but failing lh.w-g.pct.mgh Reading curvature file /scratch/lfs/aoshea/testAndrew/processedSubjects/1492/surf/lh.w-g.pct.mgh ERROR: number of vertices in /scratch/lfs/aoshea/testAndrew/processedSubjects/1492/surf/lh.w-g.pct.mgh does not match surface (128222,130849) ERROR: reading curvature file Linux c1a-s11.ufhpc 2.6.32-358.23.2.el6.x86_64 #1 SMP Sat Sep 14 05:32:37 EDT 2013 x86_64 x86_64 x86_64 GNU/Linux recon-all -s 1492 exited with ERRORS at Wed Jul 23 11:07:01 EDT 2014 Any suggestions on how to address this? Any idea of the cause? I assuming it has something to do with the manual edits since unedited ppl run fine. -Andrew ___ Freesurfer mailing list 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.
Re: [Freesurfer] Converting volume to label
Hi Bruce, Thanks for the input. Here are some of the output lines that I get when I try overlaying one of our ROI surfaces (test-eh.mgh) onto colin (we had created a copy rk, but are back to using the original as downloaded): tksurfer colin rh white -overlay /Users/../test-rh.mgh sufer: Tailrach xform file not found (ignored) -- this is as before tkmedit: Trying to open /Users/.../test-rh.dat surfer: Interpreting overlay volume /Users/.../test-rh.mgh as encoded scalar volume. MRISreadCurvature: could not open /Applications/freesurfer/.../colin/surf/rh.curv surfer: error reading curvature file surfer: tkoInitWindow(colin) reading white matter vertex locations When I place the mouse over the displayed colin surface in tksurfer, although the displayed option at the bottom is test-rh.mgh, the resultant value is ** 0.00 **. Do I need to create a test-rh.dat file? How would I go about doing that? Should my template brain colin have a curvature file? Again, thank you for any inputs or suggestions! -- Sarah From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, July 23, 2014 9:52 AM To: Freesurfer support list Subject: Re: [Freesurfer] Converting volume to label Hi Sarah Doug is out of email contact for another week or so, and this might have to wait for his return. In the meantime: are you trying to overlay it on the colin surface or on some other subject (rk?). If you load the [lr]h.white surface over the volume for colin does it look ok? cheers Bruce On Wed, 23 Jul 2014, Weiss, Sarah wrote: Hi all, We are still struggling with this issue - any ideas? Here is some more information: - The surface that we are trying to label is the subject colin, as found here: http://mindboggle.info/data.html. We get two errors when loading in tksurfer (1) surfer: Tailairach xform file not found (ignored) (2) MRISreadVertexPosition(/Applications/.../subject/colin/surf/lh.org); No such file or directory However, the surface does load and can be manipulated (a label can be created manually and filled in). - We first tried to create a surface to overlay from our .nii file (which does load in Freeview) with mri_vol2surf. Our .nii had been converted to a .mgz with a corresponding .dat file using [COMMAND]. We tried --out_type paint (with file type .w) and --out_type mgh (with file type .mgh), but both gave the same error: MRISread: file '.../surf/test-lh.w' has 0 vertices! Probably trying to use a scalar data file as a surface! - We next tried mri_cor2label --i cluster1_roi.nii --l ./cluster1.label --id 1. In Freeview with our .nii file loaded, we verified that our volume of interest does have a value of 1, and unselected regions have a value of 0. It seems to run properly, finding unassigned vertices in label and assigning vertex numbers to label. However, in tksurfer, when we select File Load label value file cluster1.label, we get the following error: sclv_load_label_value_file: error reading line 1: 9389 We have two main questions - any advice would be greatly appreciated! (1) From my understanding of label files, the first line should be the number of vertices in the label file. Why then do we get an error in reading this line when loading the label file? (2) Are the initial errors pertaining to a lack of files for our template surface going to create a problem when we do successfully load our label file? If so, is there a way to align the two in the same coordinate space? Thank you! -- Sarah Weiss From: Weiss, Sarah Sent: Friday, July 18, 2014 3:02 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Converting volume to label Dear Freesurfer experts, We are trying to convert a volume created in SPM and saved as a .nii file into a label to overlay on a Freesurfer surface. We are using a template surface found online, colin (http://mindboggle.info/data.html). We are able to display our .nii in freeview successfully. The voxels that we wish to label have a value of 1, and elsewhere in the file the value is 0. The command that we are running is: mri_cor2label --i cluster3_roi.nii --l ./cluster3_roi.label --id 1 We do get a series of points as output. However, when we load the consequent label, it doesn't display correctly - the points are discontinuous, and don't correspond to the correct parts of the brain. Here are some of the error messages that we get: ltMNIreadEx: could not open file /Applications/freesurfer/subjects/rk/mri/transforms/talairach.xfm No such file or directory MRISreadVertexPosition(/Applications/freesurfer/subjects/rk/surf/rh.orig): could not open file /Applications/freesurfer/subjects/rk/surf/rh.orig No such file or directory MRISreadOriginalProperties: could not read surface file
Re: [Freesurfer] Converting volume to label
Hi Sarah how did you create the test-rh.mgh? If you bring it up as a volume in freeview over one of the colin volumes, do they align? Do the lh.white/rh.white also align with your colin volume? Bruce p.s. can you remind me where you got the FS-processed colin data? On Wed, 23 Jul 2014, Weiss, Sarah wrote: Hi Bruce, Thanks for the input. Here are some of the output lines that I get when I try overlaying one of our ROI surfaces (test-eh.mgh) onto colin (we had created a copy rk, but are back to using the original as downloaded): tksurfer colin rh white -overlay /Users/../test-rh.mgh sufer: Tailrach xform file not found (ignored) -- this is as before tkmedit: Trying to open /Users/.../test-rh.dat surfer: Interpreting overlay volume /Users/.../test-rh.mgh as encoded scalar volume. MRISreadCurvature: could not open /Applications/freesurfer/.../colin/surf/rh.curv surfer: error reading curvature file surfer: tkoInitWindow(colin) reading white matter vertex locations When I place the mouse over the displayed colin surface in tksurfer, although the displayed option at the bottom is test-rh.mgh, the resultant value is ** 0.00 **. Do I need to create a test-rh.dat file? How would I go about doing that? Should my template brain colin have a curvature file? Again, thank you for any inputs or suggestions! -- Sarah From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, July 23, 2014 9:52 AM To: Freesurfer support list Subject: Re: [Freesurfer] Converting volume to label Hi Sarah Doug is out of email contact for another week or so, and this might have to wait for his return. In the meantime: are you trying to overlay it on the colin surface or on some other subject (rk?). If you load the [lr]h.white surface over the volume for colin does it look ok? cheers Bruce On Wed, 23 Jul 2014, Weiss, Sarah wrote: Hi all, We are still struggling with this issue - any ideas? Here is some more information: - The surface that we are trying to label is the subject colin, as found here: http://mindboggle.info/data.html. We get two errors when loading in tksurfer (1) surfer: Tailairach xform file not found (ignored) (2) MRISreadVertexPosition(/Applications/.../subject/colin/surf/lh.org); No such file or directory However, the surface does load and can be manipulated (a label can be created manually and filled in). - We first tried to create a surface to overlay from our .nii file (which does load in Freeview) with mri_vol2surf. Our .nii had been converted to a .mgz with a corresponding .dat file using [COMMAND]. We tried --out_type paint (with file type .w) and --out_type mgh (with file type .mgh), but both gave the same error: MRISread: file '.../surf/test-lh.w' has 0 vertices! Probably trying to use a scalar data file as a surface! - We next tried mri_cor2label --i cluster1_roi.nii --l ./cluster1.label --id 1. In Freeview with our .nii file loaded, we verified that our volume of interest does have a value of 1, and unselected regions have a value of 0. It seems to run properly, finding unassigned vertices in label and assigning vertex numbers to label. However, in tksurfer, when we select File Load label value file cluster1.label, we get the following error: sclv_load_label_value_file: error reading line 1: 9389 We have two main questions - any advice would be greatly appreciated! (1) From my understanding of label files, the first line should be the number of vertices in the label file. Why then do we get an error in reading this line when loading the label file? (2) Are the initial errors pertaining to a lack of files for our template surface going to create a problem when we do successfully load our label file? If so, is there a way to align the two in the same coordinate space? Thank you! -- Sarah Weiss From: Weiss, Sarah Sent: Friday, July 18, 2014 3:02 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Converting volume to label Dear Freesurfer experts, We are trying to convert a volume created in SPM and saved as a .nii file into a label to overlay on a Freesurfer surface. We are using a template surface found online, colin (http://mindboggle.info/data.html). We are able to display our .nii in freeview successfully. The voxels that we wish to label have a value of 1, and elsewhere in the file the value is 0. The command that we are running is: mri_cor2label --i cluster3_roi.nii --l ./cluster3_roi.label --id 1 We do get a series of points as output. However, when we load the consequent label, it doesn't display correctly - the points are discontinuous, and don't correspond to the correct parts of the brain. Here are some of the error messages that we get: ltMNIreadEx: could not open file
Re: [Freesurfer] Converting volume to label
Hi Bruce, To create the .mgh, we used the following command: mri_vol2surf --src cluster1_roi.mgz --srcreg cluster1_roi.dat --hemi rh --o ./test-rh.mgh --out_type mgh --float2int tkregister I can view both the .nii and the .mgz in Freeview but the /test-rh.mgh does not appear to have any nonzero vertices. Any thoughts on why this might be? From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, July 23, 2014 12:22 PM To: Freesurfer support list Subject: Re: [Freesurfer] Converting volume to label Hi Sarah how did you create the test-rh.mgh? If you bring it up as a volume in freeview over one of the colin volumes, do they align? Do the lh.white/rh.white also align with your colin volume? Bruce p.s. can you remind me where you got the FS-processed colin data? On Wed, 23 Jul 2014, Weiss, Sarah wrote: Hi Bruce, Thanks for the input. Here are some of the output lines that I get when I try overlaying one of our ROI surfaces (test-eh.mgh) onto colin (we had created a copy rk, but are back to using the original as downloaded): tksurfer colin rh white -overlay /Users/../test-rh.mgh sufer: Tailrach xform file not found (ignored) -- this is as before tkmedit: Trying to open /Users/.../test-rh.dat surfer: Interpreting overlay volume /Users/.../test-rh.mgh as encoded scalar volume. MRISreadCurvature: could not open /Applications/freesurfer/.../colin/surf/rh.curv surfer: error reading curvature file surfer: tkoInitWindow(colin) reading white matter vertex locations When I place the mouse over the displayed colin surface in tksurfer, although the displayed option at the bottom is test-rh.mgh, the resultant value is ** 0.00 **. Do I need to create a test-rh.dat file? How would I go about doing that? Should my template brain colin have a curvature file? Again, thank you for any inputs or suggestions! -- Sarah From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, July 23, 2014 9:52 AM To: Freesurfer support list Subject: Re: [Freesurfer] Converting volume to label Hi Sarah Doug is out of email contact for another week or so, and this might have to wait for his return. In the meantime: are you trying to overlay it on the colin surface or on some other subject (rk?). If you load the [lr]h.white surface over the volume for colin does it look ok? cheers Bruce On Wed, 23 Jul 2014, Weiss, Sarah wrote: Hi all, We are still struggling with this issue - any ideas? Here is some more information: - The surface that we are trying to label is the subject colin, as found here: http://mindboggle.info/data.html. We get two errors when loading in tksurfer (1) surfer: Tailairach xform file not found (ignored) (2) MRISreadVertexPosition(/Applications/.../subject/colin/surf/lh.org); No such file or directory However, the surface does load and can be manipulated (a label can be created manually and filled in). - We first tried to create a surface to overlay from our .nii file (which does load in Freeview) with mri_vol2surf. Our .nii had been converted to a .mgz with a corresponding .dat file using [COMMAND]. We tried --out_type paint (with file type .w) and --out_type mgh (with file type .mgh), but both gave the same error: MRISread: file '.../surf/test-lh.w' has 0 vertices! Probably trying to use a scalar data file as a surface! - We next tried mri_cor2label --i cluster1_roi.nii --l ./cluster1.label --id 1. In Freeview with our .nii file loaded, we verified that our volume of interest does have a value of 1, and unselected regions have a value of 0. It seems to run properly, finding unassigned vertices in label and assigning vertex numbers to label. However, in tksurfer, when we select File Load label value file cluster1.label, we get the following error: sclv_load_label_value_file: error reading line 1: 9389 We have two main questions - any advice would be greatly appreciated! (1) From my understanding of label files, the first line should be the number of vertices in the label file. Why then do we get an error in reading this line when loading the label file? (2) Are the initial errors pertaining to a lack of files for our template surface going to create a problem when we do successfully load our label file? If so, is there a way to align the two in the same coordinate space? Thank you! -- Sarah Weiss From: Weiss, Sarah Sent: Friday, July 18, 2014 3:02 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Converting volume to label Dear Freesurfer experts, We are trying to convert a volume created in SPM and saved as a .nii file into a label to overlay on a
Re: [Freesurfer] Converting volume to label
Hi Sarah how did you create cluster1_roi.mgz? Is it in register with colin? Bruce On Wed, 23 Jul 2014, Weiss, Sarah wrote: Hi Bruce, To create the .mgh, we used the following command: mri_vol2surf --src cluster1_roi.mgz --srcreg cluster1_roi.dat --hemi rh --o ./test-rh.mgh --out_type mgh --float2int tkregister I can view both the .nii and the .mgz in Freeview but the /test-rh.mgh does not appear to have any nonzero vertices. Any thoughts on why this might be? From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, July 23, 2014 12:22 PM To: Freesurfer support list Subject: Re: [Freesurfer] Converting volume to label Hi Sarah how did you create the test-rh.mgh? If you bring it up as a volume in freeview over one of the colin volumes, do they align? Do the lh.white/rh.white also align with your colin volume? Bruce p.s. can you remind me where you got the FS-processed colin data? On Wed, 23 Jul 2014, Weiss, Sarah wrote: Hi Bruce, Thanks for the input. Here are some of the output lines that I get when I try overlaying one of our ROI surfaces (test-eh.mgh) onto colin (we had created a copy rk, but are back to using the original as downloaded): tksurfer colin rh white -overlay /Users/../test-rh.mgh sufer: Tailrach xform file not found (ignored) -- this is as before tkmedit: Trying to open /Users/.../test-rh.dat surfer: Interpreting overlay volume /Users/.../test-rh.mgh as encoded scalar volume. MRISreadCurvature: could not open /Applications/freesurfer/.../colin/surf/rh.curv surfer: error reading curvature file surfer: tkoInitWindow(colin) reading white matter vertex locations When I place the mouse over the displayed colin surface in tksurfer, although the displayed option at the bottom is test-rh.mgh, the resultant value is ** 0.00 **. Do I need to create a test-rh.dat file? How would I go about doing that? Should my template brain colin have a curvature file? Again, thank you for any inputs or suggestions! -- Sarah From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, July 23, 2014 9:52 AM To: Freesurfer support list Subject: Re: [Freesurfer] Converting volume to label Hi Sarah Doug is out of email contact for another week or so, and this might have to wait for his return. In the meantime: are you trying to overlay it on the colin surface or on some other subject (rk?). If you load the [lr]h.white surface over the volume for colin does it look ok? cheers Bruce On Wed, 23 Jul 2014, Weiss, Sarah wrote: Hi all, We are still struggling with this issue - any ideas? Here is some more information: - The surface that we are trying to label is the subject colin, as found here: http://mindboggle.info/data.html. We get two errors when loading in tksurfer (1) surfer: Tailairach xform file not found (ignored) (2) MRISreadVertexPosition(/Applications/.../subject/colin/surf/lh.org); No such file or directory However, the surface does load and can be manipulated (a label can be created manually and filled in). - We first tried to create a surface to overlay from our .nii file (which does load in Freeview) with mri_vol2surf. Our .nii had been converted to a .mgz with a corresponding .dat file using [COMMAND]. We tried --out_type paint (with file type .w) and --out_type mgh (with file type .mgh), but both gave the same error: MRISread: file '.../surf/test-lh.w' has 0 vertices! Probably trying to use a scalar data file as a surface! - We next tried mri_cor2label --i cluster1_roi.nii --l ./cluster1.label --id 1. In Freeview with our .nii file loaded, we verified that our volume of interest does have a value of 1, and unselected regions have a value of 0. It seems to run properly, finding unassigned vertices in label and assigning vertex numbers to label. However, in tksurfer, when we select File Load label value file cluster1.label, we get the following error: sclv_load_label_value_file: error reading line 1: 9389 We have two main questions - any advice would be greatly appreciated! (1) From my understanding of label files, the first line should be the number of vertices in the label file. Why then do we get an error in reading this line when loading the label file? (2) Are the initial errors pertaining to a lack of files for our template surface going to create a problem when we do successfully load our label file? If so, is there a way to align the two in the same coordinate space? Thank you! -- Sarah Weiss From: Weiss, Sarah Sent: Friday, July 18, 2014 3:02 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Converting volume to
[Freesurfer] wm/pial surfaces from manually created surfaces
Greetings, I would like to use two surfaces that I created manually on the same anatomy and to create a single subject with the surfaces such that one is the pial and the other is the wm surface. Any leads on how to achieve this will be greatly appreciated. Thanks, Itamar ___ Freesurfer mailing list 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.
Re: [Freesurfer] Converting volume to label
Hi Bruce, I believe that we used the command recon-all to create cluster1_roi.mgz. When opened in freeview along with colin, it appears to be in alignment. I'm not clear on where our cluster1_roi.dat file originated from though - I'll look into that. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, July 23, 2014 1:23 PM To: Freesurfer support list Subject: Re: [Freesurfer] Converting volume to label Hi Sarah how did you create cluster1_roi.mgz? Is it in register with colin? Bruce On Wed, 23 Jul 2014, Weiss, Sarah wrote: Hi Bruce, To create the .mgh, we used the following command: mri_vol2surf --src cluster1_roi.mgz --srcreg cluster1_roi.dat --hemi rh --o ./test-rh.mgh --out_type mgh --float2int tkregister I can view both the .nii and the .mgz in Freeview but the /test-rh.mgh does not appear to have any nonzero vertices. Any thoughts on why this might be? From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, July 23, 2014 12:22 PM To: Freesurfer support list Subject: Re: [Freesurfer] Converting volume to label Hi Sarah how did you create the test-rh.mgh? If you bring it up as a volume in freeview over one of the colin volumes, do they align? Do the lh.white/rh.white also align with your colin volume? Bruce p.s. can you remind me where you got the FS-processed colin data? On Wed, 23 Jul 2014, Weiss, Sarah wrote: Hi Bruce, Thanks for the input. Here are some of the output lines that I get when I try overlaying one of our ROI surfaces (test-eh.mgh) onto colin (we had created a copy rk, but are back to using the original as downloaded): tksurfer colin rh white -overlay /Users/../test-rh.mgh sufer: Tailrach xform file not found (ignored) -- this is as before tkmedit: Trying to open /Users/.../test-rh.dat surfer: Interpreting overlay volume /Users/.../test-rh.mgh as encoded scalar volume. MRISreadCurvature: could not open /Applications/freesurfer/.../colin/surf/rh.curv surfer: error reading curvature file surfer: tkoInitWindow(colin) reading white matter vertex locations When I place the mouse over the displayed colin surface in tksurfer, although the displayed option at the bottom is test-rh.mgh, the resultant value is ** 0.00 **. Do I need to create a test-rh.dat file? How would I go about doing that? Should my template brain colin have a curvature file? Again, thank you for any inputs or suggestions! -- Sarah From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, July 23, 2014 9:52 AM To: Freesurfer support list Subject: Re: [Freesurfer] Converting volume to label Hi Sarah Doug is out of email contact for another week or so, and this might have to wait for his return. In the meantime: are you trying to overlay it on the colin surface or on some other subject (rk?). If you load the [lr]h.white surface over the volume for colin does it look ok? cheers Bruce On Wed, 23 Jul 2014, Weiss, Sarah wrote: Hi all, We are still struggling with this issue - any ideas? Here is some more information: - The surface that we are trying to label is the subject colin, as found here: http://mindboggle.info/data.html. We get two errors when loading in tksurfer (1) surfer: Tailairach xform file not found (ignored) (2) MRISreadVertexPosition(/Applications/.../subject/colin/surf/lh.org); No such file or directory However, the surface does load and can be manipulated (a label can be created manually and filled in). - We first tried to create a surface to overlay from our .nii file (which does load in Freeview) with mri_vol2surf. Our .nii had been converted to a .mgz with a corresponding .dat file using [COMMAND]. We tried --out_type paint (with file type .w) and --out_type mgh (with file type .mgh), but both gave the same error: MRISread: file '.../surf/test-lh.w' has 0 vertices! Probably trying to use a scalar data file as a surface! - We next tried mri_cor2label --i cluster1_roi.nii --l ./cluster1.label --id 1. In Freeview with our .nii file loaded, we verified that our volume of interest does have a value of 1, and unselected regions have a value of 0. It seems to run properly, finding unassigned vertices in label and assigning vertex numbers to label. However, in tksurfer, when we select File Load label value file cluster1.label, we get the following error: sclv_load_label_value_file: error reading line 1: 9389 We have two main questions - any advice would be greatly appreciated! (1) From my understanding of label files, the first line should be the number of
Re: [Freesurfer] Converting volume to label
if it's in alignment without the .dat file you probably shouldn't use the dat file in the sampling onto the surface. I don't think it was created by recon-all though cheers Bruce On Wed, 23 Jul 2014, Weiss, Sarah wrote: Hi Bruce, I believe that we used the command recon-all to create cluster1_roi.mgz. When opened in freeview along with colin, it appears to be in alignment. I'm not clear on where our cluster1_roi.dat file originated from though - I'll look into that. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, July 23, 2014 1:23 PM To: Freesurfer support list Subject: Re: [Freesurfer] Converting volume to label Hi Sarah how did you create cluster1_roi.mgz? Is it in register with colin? Bruce On Wed, 23 Jul 2014, Weiss, Sarah wrote: Hi Bruce, To create the .mgh, we used the following command: mri_vol2surf --src cluster1_roi.mgz --srcreg cluster1_roi.dat --hemi rh --o ./test-rh.mgh --out_type mgh --float2int tkregister I can view both the .nii and the .mgz in Freeview but the /test-rh.mgh does not appear to have any nonzero vertices. Any thoughts on why this might be? From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, July 23, 2014 12:22 PM To: Freesurfer support list Subject: Re: [Freesurfer] Converting volume to label Hi Sarah how did you create the test-rh.mgh? If you bring it up as a volume in freeview over one of the colin volumes, do they align? Do the lh.white/rh.white also align with your colin volume? Bruce p.s. can you remind me where you got the FS-processed colin data? On Wed, 23 Jul 2014, Weiss, Sarah wrote: Hi Bruce, Thanks for the input. Here are some of the output lines that I get when I try overlaying one of our ROI surfaces (test-eh.mgh) onto colin (we had created a copy rk, but are back to using the original as downloaded): tksurfer colin rh white -overlay /Users/../test-rh.mgh sufer: Tailrach xform file not found (ignored) -- this is as before tkmedit: Trying to open /Users/.../test-rh.dat surfer: Interpreting overlay volume /Users/.../test-rh.mgh as encoded scalar volume. MRISreadCurvature: could not open /Applications/freesurfer/.../colin/surf/rh.curv surfer: error reading curvature file surfer: tkoInitWindow(colin) reading white matter vertex locations When I place the mouse over the displayed colin surface in tksurfer, although the displayed option at the bottom is test-rh.mgh, the resultant value is ** 0.00 **. Do I need to create a test-rh.dat file? How would I go about doing that? Should my template brain colin have a curvature file? Again, thank you for any inputs or suggestions! -- Sarah From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl [fis...@nmr.mgh.harvard.edu] Sent: Wednesday, July 23, 2014 9:52 AM To: Freesurfer support list Subject: Re: [Freesurfer] Converting volume to label Hi Sarah Doug is out of email contact for another week or so, and this might have to wait for his return. In the meantime: are you trying to overlay it on the colin surface or on some other subject (rk?). If you load the [lr]h.white surface over the volume for colin does it look ok? cheers Bruce On Wed, 23 Jul 2014, Weiss, Sarah wrote: Hi all, We are still struggling with this issue - any ideas? Here is some more information: - The surface that we are trying to label is the subject colin, as found here: http://mindboggle.info/data.html. We get two errors when loading in tksurfer (1) surfer: Tailairach xform file not found (ignored) (2) MRISreadVertexPosition(/Applications/.../subject/colin/surf/lh.org); No such file or directory However, the surface does load and can be manipulated (a label can be created manually and filled in). - We first tried to create a surface to overlay from our .nii file (which does load in Freeview) with mri_vol2surf. Our .nii had been converted to a .mgz with a corresponding .dat file using [COMMAND]. We tried --out_type paint (with file type .w) and --out_type mgh (with file type .mgh), but both gave the same error: MRISread: file '.../surf/test-lh.w' has 0 vertices! Probably trying to use a scalar data file as a surface! - We next tried mri_cor2label --i cluster1_roi.nii --l ./cluster1.label --id 1. In Freeview with our .nii file loaded, we verified that our volume of interest does have a value of 1, and unselected regions have a value of 0. It seems to run properly, finding unassigned vertices in label and assigning vertex numbers to label. However, in tksurfer, when we select File Load label value file
[Freesurfer] Calculate average thickness mathematically?
Hi all, A while ago I asked how can I calculate the average thickness of the three lateral temporal gyri, and Bruce kindly suggested to draw the label on fsaverage and use transforms to calculate it for each subject. I may try to do that, but given my time constrains and my level of knowledge of Freesurger I thought an alternative method: Say for example I have the inferior, middle, and superior temporal gyrus with surface areas of 1000, 2000, and 3000. They also have an average thickness of 2, 3, and 4mm, respectively. Given that these thicknesses are distributed in those areas, I could weight each region accordingly and calculate the average thickness as: ( (1000*2) + (2000*3) + (3000*4) ) / (1000+2000+3000) = 2/6000 = 3.33 Is this logic correct, and why yes or no? Thank you in advance. Dorian TJU ___ Freesurfer mailing list 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.
[Freesurfer] Mapping stats into volume with mri_label2vol
Hello all, I am trying to map polar angle and eccentricity into the voxels underneath a particular label. For each vertex in the label file, I’ve put in the respective angle in the stats column. I then used mri_label2vol with the --label-stat flag to map the angle values into the volume. Comparing the angle values for each individual voxel and each vertex, I’ve noticed that some values that are in the voxels are not present in the vertices (ie a particular voxel might have a value of 0.5 but none of the vertices have that exact value). What happens when the values are mapped from the vertex into the volume? Is there some averaging or weighting process or something? Many thanks, jack ___ Freesurfer mailing list 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.
Re: [Freesurfer] question regarding control point edits
Hi Bruce, Yeah that was my thinking as well. So, if after running 500 subjects through FS and 100 need similar edits in the anterior temporal lobes, we will have no choice but to perform manual edits for each case individually? Thanks for clarifying! Adam Mezher Hi Adam I don't think so as how would we don't know where the anterior temporal lobe at that stage in the process. Bruce On Tue, 22 Jul 2014, Adam Mezher wrote: Hi FreeSurfer group, I was wondering if there is a way to include control points in my command line when I run recon-all. We are working with a large dataset and many of the subjects have underestimations in the anterior temporal lobes so it would be beneficial to expand the WM surface slightly on numerous cases rather than doing control point edits on each case individually. Thank you, Adam Mezher ___ Freesurfer mailing list 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.
Re: [Freesurfer] question regarding control point edits
Hi Adam it depends on the source of the bias. If it is fixed in the coordinate system of the scanner you could correct a few, then try using mri_compute_bias and mri_apply_bias to see if it helps (it computes an average bias field in scanner coords, then applies it to a new dataset) cheers Bruce On Wed, 23 Jul 2014, Adam Mezher wrote: Hi Bruce, Yeah that was my thinking as well. So, if after running 500 subjects through FS and 100 need similar edits in the anterior temporal lobes, we will have no choice but to perform manual edits for each case individually? Thanks for clarifying! Adam Mezher Hi Adam I don't think so as how would we don't know where the anterior temporal lobe at that stage in the process. Bruce On Tue, 22 Jul 2014, Adam Mezher wrote: Hi FreeSurfer group, I was wondering if there is a way to include control points in my command line when I run recon-all. We are working with a large dataset and many of the subjects have underestimations in the anterior temporal lobes so it would be beneficial to expand the WM surface slightly on numerous cases rather than doing control point edits on each case individually. Thank you, Adam Mezher ___ Freesurfer mailing list 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.
Re: [Freesurfer] Calculate average thickness mathematically?
Hi Dorian yes, that would work. cheers Bruce On Wed, 23 Jul 2014, Dorian P. wrote: Hi all, A while ago I asked how can I calculate the average thickness of the three lateral temporal gyri, and Bruce kindly suggested to draw the label on fsaverage and use transforms to calculate it for each subject. I may try to do that, but given my time constrains and my level of knowledge of Freesurger I thought an alternative method: Say for example I have the inferior, middle, and superior temporal gyrus with surface areas of 1000, 2000, and 3000. They also have an average thickness of 2, 3, and 4mm, respectively. Given that these thicknesses are distributed in those areas, I could weight each region accordingly and calculate the average thickness as: ( (1000*2) + (2000*3) + (3000*4) ) / (1000+2000+3000) = 2/6000 = 3.33 Is this logic correct, and why yes or no? Thank you in advance. Dorian TJU ___ Freesurfer mailing list 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.
[Freesurfer] Question with QDEC annotations and mri_convert and mri_annotation2label
Hello, I am trying to convert my significant cluster from qdec into a .gii file, and I have a couple of questions. My mri_convert is not working, but it is my first time using it so I may be missing something, but it just keeps opening up the usage and gives no errors. mris_convert --annot mc-z.abs.th13.sig.ocn.annot mc-z.abs.th13.sig.ocn.gii Also, I was curious, how would one separate a annotation file created in qdec into separate label files with mri_annotation2label since there is no target subject which is required in he script. Thanks! Tara ___ Freesurfer mailing list 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.
Re: [Freesurfer] Questions regarding recon-all command
Hi Bruce, Thanks a lot for replying. The original data comes in .nii.gz format but when I unzipped it it become .hdr-.img (2 files). The freeSurfer is not understanding the .hdr-.img format but I am able to run it using .nii.gz format. Thanks you again, Soumya. From: freesurfer-boun...@nmr.mgh.harvard.edu freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl fis...@nmr.mgh.harvard.edu Sent: Wednesday, July 23, 2014 2:11 AM To: Freesurfer support list Subject: Re: [Freesurfer] Questions regarding recon-all command Hi Soumya Can you include the full command and screen output of what you ran? Are you sure that they are nifti and not analyze? Analyze is to be avoided as it doesn't contain enough information to tell left from right Cheers Bruce On Jul 22, 2014, at 8:01 PM, soumyabrata.dey soumyabrata@knights.ucf.edumailto:soumyabrata@knights.ucf.edu wrote: ?Hi All, I am new to freeSurfer and need your guidance for some of the doubts I have. I have installed freeSurfer in a windows 7 machine using virtualBox. I am trying to process some of my own sMRI data using freeSurfer software. The data is skull-stripped and has cerebellum. The format of the data is NIFTI (.hdr, .img). I am having some problem with running the recon-all command on the data as I am getting the error message saying filename.hdr is not found (I have also tried with inputting .img file). My questions are: * ?Is recon-all compatible with .hdr .img file format? I know it should run with .dcm and .nii files. If not what are my option? * ?Do I need to set up any environment variable for the -i option of the recon-all like the SUBJECTS-DIR for -s option. I have tried inputting the full path of the input file. Also, I tried with moving to the directory of input file and run the command from there. Thanks for your help, Soumya. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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 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.
Re: [Freesurfer] Questions regarding recon-all command
yes, there is no need to unzip it, we read gzipped nifti just fine Bruce On Wed, 23 Jul 2014, soumyabrata.dey wrote: Hi Bruce, Thanks a lot for replying. The original data comes in .nii.gz format but when I unzipped it it become .hdr-.img (2 files). The freeSurfer is not understanding the .hdr-.img format but I am able to run it using .nii.gz format. Thanks you again, Soumya. From: freesurfer-boun...@nmr.mgh.harvard.edu freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl fis...@nmr.mgh.harvard.edu Sent: Wednesday, July 23, 2014 2:11 AM To: Freesurfer support list Subject: Re: [Freesurfer] Questions regarding recon-all command Hi Soumya Can you include the full command and screen output of what you ran? Are you sure that they are nifti and not analyze? Analyze is to be avoided as it doesn't contain enough information to tell left from right Cheers Bruce On Jul 22, 2014, at 8:01 PM, soumyabrata.dey soumyabrata@knights.ucf.edu wrote: Hi All, I am new to freeSurfer and need your guidance for some of the doubts I have. I have installed freeSurfer in a windows 7 machine using virtualBox. I am trying to process some of my own sMRI data using freeSurfer software. The data is skull-stripped and has cerebellum. The format of the data is NIFTI (.hdr, .img). I am having some problem with running the recon-all command on the data as I am getting the error message saying filename.hdr is not found (I have also tried with inputting .img file). My questions are: o Is recon-all compatible with .hdr .img file format? I know it should run with .dcm and .nii files. If not what are my option? o Do I need to set up any environment variable for the -i option of the recon-all like the SUBJECTS-DIR for -s option. I have tried inputting the full path of the input file. Also, I tried with moving to the directory of input file and run the command from there. Thanks for your help, Soumya. ___ 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 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.
Re: [Freesurfer] Calculate average thickness mathematically?
Thanks Bruce, this is going to be very helpful. One thing I have not understood from the statistics freesurfer outputs is why average thickness is not exactly the ratio between volume and surface area. This is just a small curiosity though. Best regards. Dorian On Jul 23, 2014 3:40 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Dorian yes, that would work. cheers Bruce On Wed, 23 Jul 2014, Dorian P. wrote: Hi all, A while ago I asked how can I calculate the average thickness of the three lateral temporal gyri, and Bruce kindly suggested to draw the label on fsaverage and use transforms to calculate it for each subject. I may try to do that, but given my time constrains and my level of knowledge of Freesurger I thought an alternative method: Say for example I have the inferior, middle, and superior temporal gyrus with surface areas of 1000, 2000, and 3000. They also have an average thickness of 2, 3, and 4mm, respectively. Given that these thicknesses are distributed in those areas, I could weight each region accordingly and calculate the average thickness as: ( (1000*2) + (2000*3) + (3000*4) ) / (1000+2000+3000) = 2/6000 = 3.33 Is this logic correct, and why yes or no? Thank you in advance. Dorian TJU ___ Freesurfer mailing list 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. ___ Freesurfer mailing list 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.
