[Freesurfer] (no subject)
Could someone please tell me how to unsubscribe from this list? I couldn't find it on the website. Thanks On Jul 2, 2015 4:56 AM, Milde, Christopher christopher.mi...@zi-mannheim.de wrote: Dear Freesurfers, I have problems converting .nii.gz files into .mgh files needed e.g. for performing ROI analysis. I used mri_vol2surf and mri_vol2vol to produce .mgh files either to visualize contrast estimates and significance maps on volumes or surfaces I think the problem is due to voxel resolution mismatches between source and registration files but I don't know how to solve this problem. I worked with different registration files: the register.dof6.dat (originally outpu from the preproc-sess) as well as register.dat and register.lta by running bbregister for the template.nii.gz --- here is an example command: # resample to surface mri_vol2surf --mov $sub/bold/EX.sm5.lh/EX/sig.nii.gz --reg $sub/bold/register.lta --projfrac 0.5 \ --interp nearest --hemi lh --o $sub/bold/lh.sig.mgh mri_vol2surf --mov $sub/bold/EX.sm5.lh/EX/sig.nii.gz --reg $sub/bold/register.lta --projfrac 0.5 \ --interp nearest --hemi lh --o $sub/bold/lh.sig.mgh srcvol = PM_04001/bold/EX.sm5.lh/EX/sig.nii.gz srcreg = PM_04001/bold/register.lta srcregold = 0 srcwarp unspecified surf = white hemi = lh ProjFrac = 0.5 thickness = thickness reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 Done loading volume regio_read_register: loading lta reading extra input line subject PM_04001 reading extra input line fscale 0.15 WARNING: the voxel resolution in the source volume (1,1,1) differs from that listed in the registration file (2.29167,2.29167,2.99) Reading surface /home/christopher/subjects/PM_04001/surf/lh.white Done reading source surface Reading thickness /home/christopher/subjects/PM_04001/surf/lh.thickness Done Mapping Source Volume onto Source Subject Surface 1 0.5 0.5 0.5 using old Done mapping volume to surface Number of source voxels hit = 5 Writing to PM_04001/bold/lh.sig.mgh Dim: 126553 1 1 Thanks, Christopher ___ 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] major lobes
Thanks a lot! it worked :) -M On 12/04/2013 11:52 AM, Douglas N Greve wrote: mri_annotation2label --subject P2 --hemi lh --ctab new_ColorTable.txt --lobesStrict freeSurfer_Results/P2/label/lh.freeSurfer_lobes.annot ___ 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] major lobes
Thanks Doug! maybe I'm making this too complicated! What I want is to know which label (number) corresponds to each of the main lobes. Right now my freeSurfer_lobes.nii.gz image has lables in the range of 0-100's (which is WM if not mistaken), and then labels in the range of 1000-1035 for the left and 2000-2035 for the right hemisphere with zero labels in 1002,1008-1035 2002,2008-2035! (and these labels correspond to the GM, correct?!) I tried --ctab option by running the following command: mri_annotation2label --subject P2 --hemi lh --ctab new_ColorTable.txt --lobesStrict freeSurfer_Results/P2/label/lh.freeSurfer_lobes.annot but it's not saving anything! Could you please tell me how to properly use this option? Thanks again, -Mojdeh On 11/29/2013 04:28 PM, Douglas Greve wrote: The commands look right and it sounds like you might have the right result. What do you mean you are getting a detailed WM + GM segmentation? If you just load freeSurfer_lobes.nii.gz into tkmedit, the label names will be all messed up because you don't have the proper color table, but you should still only get 7 per hemi. To get the proper color table, run mri_annotation2label with --ctab, then merge the two ctabs you get (lh and rh). You don't need to rerun mri_aparc2aseg doug On 11/29/13 3:09 PM, Mojdeh Zamyadi wrote: Hi all, Since I haven't heard back about my question so far, I'm posting it again! Sorry about this but I really need your help! As mentioned in my previous posts, I'm interested in having the GM volumetric lobar masks (frontal, parietal, temporal, occipital, and insular) with the final goal of moving them the DTI space to perform thalamic parcellation. I've ran the following commands: 1- a. mri_annotation2label --subject P2 --hemi lh --lobesStrict freeSurfer_Results/P2/label/lh.freeSurfer_lobes.annot b. mri_annotation2label --subject P2 --hemi rh --lobesStrict freeSurfer_Results/P2/label/rh.freeSurfer_lobes.annot 2- mri_aparc2aseg --annot freeSurfer_lobes --s P2 --o freeSurfer_Results/P2/label/freeSurfer_lobes.nii.gz I thought after doing this I'm going to get the 5 or 6 lobar labels, but instead I'm getting a detailed WM + GM segmentation. I looked at FreeSurferColorLUT.txt and tried to manually combine labels in the range of 1000-1035 for the left and 2000-2035 for the right hemisphere to get the lobe masks, but after having a closer look I realised that labels 1002,1008-1035 2002,2008-2035 are all empty (ie. I only have 7 labels in each hemisphere)! so, I'm now not sure how to manually combine these labels either! Could someone PLEASE PLEASE clarify this for me! I would really appreciate any help! Thanks, -Mojdeh ___ 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
[Freesurfer] major lobes
Hi all, Since I haven't heard back about my question so far, I'm posting it again! Sorry about this but I really need your help! As mentioned in my previous posts, I'm interested in having the GM volumetric lobar masks (frontal, parietal, temporal, occipital, and insular) with the final goal of moving them the DTI space to perform thalamic parcellation. I've ran the following commands: 1- a. mri_annotation2label --subject P2 --hemi lh --lobesStrict freeSurfer_Results/P2/label/lh.freeSurfer_lobes.annot b. mri_annotation2label --subject P2 --hemi rh --lobesStrict freeSurfer_Results/P2/label/rh.freeSurfer_lobes.annot 2- mri_aparc2aseg --annot freeSurfer_lobes --s P2 --o freeSurfer_Results/P2/label/freeSurfer_lobes.nii.gz I thought after doing this I'm going to get the 5 or 6 lobar labels, but instead I'm getting a detailed WM + GM segmentation. I looked at FreeSurferColorLUT.txt and tried to manually combine labels in the range of 1000-1035 for the left and 2000-2035 for the right hemisphere to get the lobe masks, but after having a closer look I realised that labels 1002,1008-1035 2002,2008-2035 are all empty (ie. I only have 7 labels in each hemisphere)! so, I'm now not sure how to manually combine these labels either! Could someone PLEASE PLEASE clarify this for me! I would really appreciate any help! Thanks, -Mojdeh ___ 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 cortical labels into volumetric ROIs
Hi all, I would like to follow up on my question! So, I figured it's not really necessary to move the labels into their native space, since my final goal is to have the ROIs in the DTI (B0) space. So, I directly registered the nu-corrected output from freeSurfer to my B0 image, am I correct? But, I still don't know how to get the correct lobar masks! as mentioned before, I tried the following command: mri_aparc2aseg --annot freeSurfer_lobes --s P2 --o freeSurfer_Results/P2/label/freeSurfer_lobes.nii.gz But, it's not giving me lobe masks and instead it creates a very detailed segmentation, although I'm using an annoation file (freeSurfer_lobes) which was created using mri_annotation2label with the --lobesStrict option. Could someone please help me with how to get the grey matter lobar (frontal, parietal, temporal, occipital, and insular) masks. Thanks, -Mojdeh On 11/21/2013 04:32 PM, Mojdeh Zamyadi wrote: Thanks! so this is the command I've used: mri_aparc2aseg --annot freeSurfer_lobes --s P2 --o freeSurfer_Results/P2/labels/freeSurfer_lobes.nii.gz a couple of question I have now: 1. what lables (numbers) correspond to the 5 main lobes? looking at the FreeSurferColorLUT.txt, I'm assuming the lables I'm interested in are in the range of 1000-1035 (left) and 2000-2035 (right), is this correct? should I now manually add the relevant sections to get the 5 lobes?! or is there an automated way to do this?! 2. also, with mri_label2vol I was using the registration flags to move the labels into the native subject space, but this way (using mri_aparc2aseg) I get the labels in the freeSurfer space! are there options to move the lables? or should I do it as a separate step? if so, could you please tell me which command I should use? sorry for bugging you with so many questions! -M On 11/21/2013 01:42 PM, Douglas N Greve wrote: use mri_aparc2aseg instead of label2vol. This is how aparc+aseg.mgz is created. Look in the recon-all.log file for the command line used. doug On 11/21/2013 10:44 AM, Mojdeh Zamyadi wrote: Hi all, I want to convert the cortical labels I get in freeSurfer to volumetric ROIs in the subject space and I've followed the steps mentioned in: http://brainybehavior.com/neuroimaging/2010/05/converting-cortical-labels-from-freesurfer-to-volumetric-masks/ except since I'm interested in lobe mapping I've changed the first commands, more specifically these are the different command I've run: 1. mri_annotation2label --subject P2 --hemi lh --outdir freeSurfer_Results/P2/labels/ --lobesStrict freeSurfer_Results/P2/labels/freeSurfer_lobes 2. mri_annotation2label --hemi lh --subject P2 --outdir freeSurfer_Results/P2/labels/ --annotation freeSurfer_Results/P2/labels/lh.freeSurfer_lobes.annot 3. tkregister2 --mov freeSurfer_Results/P2/mri/rawavg.mgz --noedit --s P2 --regheader --reg freeSurfer_Results/P2/register.dat 4. mri_label2vol --label freeSurfer_Results/P2/labels/lh.parietal.label --temp freeSurfer_Results/P2/mri/rawavg.mgz --subject P2 --hemi lh --o freeSurfer_Results/P2/labels/lh.parietal.nii.gz --proj frac 0 1 .1 --fillthresh 1 --reg freeSurfer_Results/P2/register.dat the issue I have now is that the final ROI I get (e.g. lh.parietal.nii.gz) looks like a series of disconnected points! I was wondering how I can get a smooth (i.e. filled) volumetric ROI? Thanks, -Mojdeh ___ 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.
[Freesurfer] converting cortical labels into volumetric ROIs
Hi all, I want to convert the cortical labels I get in freeSurfer to volumetric ROIs in the subject space and I've followed the steps mentioned in: http://brainybehavior.com/neuroimaging/2010/05/converting-cortical-labels-from-freesurfer-to-volumetric-masks/ except since I'm interested in lobe mapping I've changed the first commands, more specifically these are the different command I've run: 1. mri_annotation2label --subject P2 --hemi lh --outdir freeSurfer_Results/P2/labels/ --lobesStrict freeSurfer_Results/P2/labels/freeSurfer_lobes 2. mri_annotation2label --hemi lh --subject P2 --outdir freeSurfer_Results/P2/labels/ --annotation freeSurfer_Results/P2/labels/lh.freeSurfer_lobes.annot 3. tkregister2 --mov freeSurfer_Results/P2/mri/rawavg.mgz --noedit --s P2 --regheader --reg freeSurfer_Results/P2/register.dat 4. mri_label2vol --label freeSurfer_Results/P2/labels/lh.parietal.label --temp freeSurfer_Results/P2/mri/rawavg.mgz --subject P2 --hemi lh --o freeSurfer_Results/P2/labels/lh.parietal.nii.gz --proj frac 0 1 .1 --fillthresh 1 --reg freeSurfer_Results/P2/register.dat the issue I have now is that the final ROI I get (e.g. lh.parietal.nii.gz) looks like a series of disconnected points! I was wondering how I can get a smooth (i.e. filled) volumetric ROI? Thanks, -Mojdeh ___ 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 cortical labels into volumetric ROIs
Thanks! so this is the command I've used: mri_aparc2aseg --annot freeSurfer_lobes --s P2 --o freeSurfer_Results/P2/labels/freeSurfer_lobes.nii.gz a couple of question I have now: 1. what lables (numbers) correspond to the 5 main lobes? looking at the FreeSurferColorLUT.txt, I'm assuming the lables I'm interested in are in the range of 1000-1035 (left) and 2000-2035 (right), is this correct? should I now manually add the relevant sections to get the 5 lobes?! or is there an automated way to do this?! 2. also, with mri_label2vol I was using the registration flags to move the labels into the native subject space, but this way (using mri_aparc2aseg) I get the labels in the freeSurfer space! are there options to move the lables? or should I do it as a separate step? if so, could you please tell me which command I should use? sorry for bugging you with so many questions! -M On 11/21/2013 01:42 PM, Douglas N Greve wrote: use mri_aparc2aseg instead of label2vol. This is how aparc+aseg.mgz is created. Look in the recon-all.log file for the command line used. doug On 11/21/2013 10:44 AM, Mojdeh Zamyadi wrote: Hi all, I want to convert the cortical labels I get in freeSurfer to volumetric ROIs in the subject space and I've followed the steps mentioned in: http://brainybehavior.com/neuroimaging/2010/05/converting-cortical-labels-from-freesurfer-to-volumetric-masks/ except since I'm interested in lobe mapping I've changed the first commands, more specifically these are the different command I've run: 1. mri_annotation2label --subject P2 --hemi lh --outdir freeSurfer_Results/P2/labels/ --lobesStrict freeSurfer_Results/P2/labels/freeSurfer_lobes 2. mri_annotation2label --hemi lh --subject P2 --outdir freeSurfer_Results/P2/labels/ --annotation freeSurfer_Results/P2/labels/lh.freeSurfer_lobes.annot 3. tkregister2 --mov freeSurfer_Results/P2/mri/rawavg.mgz --noedit --s P2 --regheader --reg freeSurfer_Results/P2/register.dat 4. mri_label2vol --label freeSurfer_Results/P2/labels/lh.parietal.label --temp freeSurfer_Results/P2/mri/rawavg.mgz --subject P2 --hemi lh --o freeSurfer_Results/P2/labels/lh.parietal.nii.gz --proj frac 0 1 .1 --fillthresh 1 --reg freeSurfer_Results/P2/register.dat the issue I have now is that the final ROI I get (e.g. lh.parietal.nii.gz) looks like a series of disconnected points! I was wondering how I can get a smooth (i.e. filled) volumetric ROI? Thanks, -Mojdeh ___ 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.
[Freesurfer] lobe mapping
Hi all, I'm interested in getting a lobar segmentation of the cortex and I've already ran recon-all on my subjects. I'm now confused by the outputs and was wondering if someone could tell me which output file contains segmentation that can be merged to get a 4 lobe parcellation similar to: http://freesurfer.net/fswiki/CorticalParcellation? Thanks a lot, -Mojdeh ___ 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] lobe mapping
Thanks a lot for the very quick reply! does this look OK? mri_annotation2label --subject P2 --hemi rh --outdir freeSurfer_Results/P2/moj_labels/ --lobesStrict freeSurfer_Results/P2/moj_labels/freeSurfer_lobes how can I convert the annotation file to nii.gz?! also, could please explain a bit what the aseg file contains? because I though that file had the complete sub-cortical parcellation (including different parts of different lobes!) sorry if my questions are rather basic, I'm very new to freeSurfer -M On 11/19/2013 11:21 AM, Douglas N Greve wrote: Try running mri_annotation2label with the --lobesStrict option doug On 11/19/2013 11:15 AM, Mojdeh Zamyadi wrote: Hi all, I'm interested in getting a lobar segmentation of the cortex and I've already ran recon-all on my subjects. I'm now confused by the outputs and was wondering if someone could tell me which output file contains segmentation that can be merged to get a 4 lobe parcellation similar to: http://freesurfer.net/fswiki/CorticalParcellation? Thanks a lot, -Mojdeh ___ 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.
[Freesurfer] extracting hippocampus volume using asegstats2table
Hi all, I have a question about the volume of the hippocampus. I want to know why when I convert the left and right hippocampus from mgz to nii (after extracting the labels from aseg.mgz) the number of voxels in the masks don't match the number I get from the asegstats2table (using --segno 17 and 53)? below are some examples numbers, the first column is the hippocampal volume using asegstats2table, and 2nd column is the volume as extracted from aseg.mgz and then converted to nii: 5157 5368 4821 4968 4858 5075 5678 5716 4970 5068 ___ 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] space of T1.mgz
Hi there, Sorry, if my question is confusing. This is what I want to do, I have two groups of controls and patients and I've already run recon-all on them. I now want to know the head/body/tail volumes. What I did was: 1. used mri_binarize to get the right and left hippocampal masks from the cortical segmentation (using label numbers 17, 53) 2. used mri_convert to convert left_hippo.mgz, right_hippo.mgz and T1.mgz into .nii files. 3. use itk SNAP to manually segment the total hippocampus (the freesurfer mask) into head, body and tail. now, my questions is regarding the last step. If the individual segmentations are in the native space, I can't be sure that the landmarks I'm using for head/body/tail separation is always the same (since some of the subjects might be in an oblique space). So would you recommend that I first register the T1 and segmentations all into a common space? Also, I was wondering if the segmentation is going to effect the actual volume (since the brain is going to be stretched and transformed while doing the registration). I hope I made my question clear and I would greatly appreciate your advice. Thanks, -Mojdeh On 12/18/2012 12:58 PM, Bruce Fischl wrote: Hi Mojdeh they are not in atlas space and the volumes are for that subject, so you shouldn't have to do anything if I understand you correctly cheers Bruce On Tue, 18 Dec 2012, Mojdeh Zamyadi wrote: Hi Doug, Thanks for the quick reply. I actually saw this link before first posting my question but it doesn't quite answer my question. What I want to know is whether the T1.mgz aseg.mgz files are in an atlas space? if that's the case, it means the segmentation for all my subjects are in the same space and I don't need to convert anything if I want to compare their hippocampal volumes. I'm not quite sure if any sort of registration to an atlas is done in any steps of recon-all or not. I would appreciate if could clarify this for me. Thanks, -Mojdeh On 12/18/2012 12:18 PM, Douglas N Greve wrote: Hi Mojdeh, try looking at this doc http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat doug On 12/18/2012 11:09 AM, Mojdeh Zamyadi wrote: Hi all, I want to segment the hippocampus into head/body/tail in itk SNAP using the hippocampus mask that I create from the result of recon-all segmentation. My question is, are the T1.mgz and aseg.mgz files in the native space of the image or in the atlas space? I know the voxel size is different (1x1x1 mm) from the original voxel size (0.49x0.49x0.45), but I want to know if the original images are registered to a common atlas space or just resampled to a different voxel size. The reason I'm asking this, is because I'm doing a group study and I want to make sure all my subjects are in the same space so that the segmentation I do is accurate for all. Thanks for your help, Mojdeh Zamyadi, MSc Clinical Research Project Assistant The Hospital for Sick Children 555 University Avenue Toronto ON M5G 1X8 ___ 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] space of T1.mgz
Hi Doug, Thanks for the quick reply. I actually saw this link before first posting my question but it doesn't quite answer my question. What I want to know is whether the T1.mgz aseg.mgz files are in an atlas space? if that's the case, it means the segmentation for all my subjects are in the same space and I don't need to convert anything if I want to compare their hippocampal volumes. I'm not quite sure if any sort of registration to an atlas is done in any steps of recon-all or not. I would appreciate if could clarify this for me. Thanks, -Mojdeh On 12/18/2012 12:18 PM, Douglas N Greve wrote: Hi Mojdeh, try looking at this doc http://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat doug On 12/18/2012 11:09 AM, Mojdeh Zamyadi wrote: Hi all, I want to segment the hippocampus into head/body/tail in itk SNAP using the hippocampus mask that I create from the result of recon-all segmentation. My question is, are the T1.mgz and aseg.mgz files in the native space of the image or in the atlas space? I know the voxel size is different (1x1x1 mm) from the original voxel size (0.49x0.49x0.45), but I want to know if the original images are registered to a common atlas space or just resampled to a different voxel size. The reason I'm asking this, is because I'm doing a group study and I want to make sure all my subjects are in the same space so that the segmentation I do is accurate for all. Thanks for your help, Mojdeh Zamyadi, MSc Clinical Research Project Assistant The Hospital for Sick Children 555 University Avenue Toronto ON M5G 1X8 ___ 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] Talairach registration
thanks Bruce :) -Mojdeh On 07/20/2012 04:27 PM, Bruce Fischl wrote: Hi Mojdeh it's really hard to say how much you should correct. In general we don't do that much. A couple of control points or a few voxels added to the wm.mgz can have a big effect if you are experienced. Mostly just see if the ?h.white and pial surface are visually accurate, and if not see if some small intervention might fix them. cheers Bruce On Fri, 20 Jul 2012, Mojdeh Zamyadi wrote: Hi Bruce, Thank's for the reply! I'm not concerned about hippocampal volume for now, mostly needing cortical thickness for my project! Yes, I am using v5.1. So in case of cortical thickness I shouldn't worry too much about Talairach registration? could you please tell me what are the main things I should check and pay attention to for cortical thickness? I'm following the troubleshooting page (http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction) and I see some discrepancies in the pial/WM surfaces but again I am not sure how much I should correct! Thanks again, -Mojdeh On 07/20/2012 04:15 PM, Bruce Fischl wrote: Hi Mojdeh it won't affect any individual thickness measures, *but* will affect the estimated total intracranial volume (eTIV). We don't typically use eTIV for thickness correction, but do for things like hippocampal volume. Are you using version 5.1? If so, that's the problem. Nick has a fix for this that he can direct you about, or you can wait for 5.2 and rerun the Talairach registration then. cheers Bruce On Fri, 20 Jul 2012, Mojdeh Zamyadi wrote: Hi all, Sorry for re-posting this but it seems it didn't get through! I've just started to do cortical thickness analysis on some subjects and I'm noticing some miss-registrations, more specifically the Talairach image is smaller than the target image no matter what subject I look at! I just wanted to make sure if this is something normal and to what extend it's going to effect the individual cortical thickness calculations. I guess I'm not sure how the Talairach transformation is used in further steps of the cortical thickness calculation. I tried to attach example coronal, sagittal and horizontal slices of one of my subjects but apparently it was too big for the mailing list. Pleas let me know if there is a way to attach images here. I greatly appreciate your advice. Thanks, Mojdeh Zamyadi, MSc Clinical Research Project Assistant The Hospital for Sick Children 555 University Avenue Toronto, ON, M5G 1X8 ___ 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] Fwd: issues with the Talairach transformation
it seems my initial message is not going through because I had some files attached! is there a way I can attach files here? thanks, -Mojdeh Original Message Subject:issues with the Talairach transformation Date: Thu, 19 Jul 2012 15:20:24 -0400 From: Mojdeh Zamyadi mojde...@gmail.com To: freesurfer@nmr.mgh.harvard.edu Hi all, I've just started to do cortical thickness analysis on some subjects and I'm noticing some miss-registrations, more specifically the Talairach image is smaller than the target image no matter what subject I look at! I just wanted to make sure if this is something normal and to what extend it's going to effect the individual cortical thickness calculations. I guess I'm not sure how the Talairach trasnformation is used in further steps of the cortical thickness calculation. I've attached example coronal, sagittal and horizontal slices of one of my subjects. I greatly appreciate your advice. Thanks, Mojdeh Zamyadi, MSc Clinical Research Project Assistant The Hospital for Sick Children 555 University Avenue Toronto ON M5G 1X8 ___ 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] Talairach registration
Hi all, Sorry for re-posting this but it seems it didn't get through! I've just started to do cortical thickness analysis on some subjects and I'm noticing some miss-registrations, more specifically the Talairach image is smaller than the target image no matter what subject I look at! I just wanted to make sure if this is something normal and to what extend it's going to effect the individual cortical thickness calculations. I guess I'm not sure how the Talairach transformation is used in further steps of the cortical thickness calculation. I tried to attach example coronal, sagittal and horizontal slices of one of my subjects but apparently it was too big for the mailing list. Pleas let me know if there is a way to attach images here. I greatly appreciate your advice. Thanks, Mojdeh Zamyadi, MSc Clinical Research Project Assistant The Hospital for Sick Children 555 University Avenue Toronto, ON, M5G 1X8 ___ 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] Talairach registration
Hi Bruce, Thank's for the reply! I'm not concerned about hippocampal volume for now, mostly needing cortical thickness for my project! Yes, I am using v5.1. So in case of cortical thickness I shouldn't worry too much about Talairach registration? could you please tell me what are the main things I should check and pay attention to for cortical thickness? I'm following the troubleshooting page (http://surfer.nmr.mgh.harvard.edu/fswiki/RecommendedReconstruction) and I see some discrepancies in the pial/WM surfaces but again I am not sure how much I should correct! Thanks again, -Mojdeh On 07/20/2012 04:15 PM, Bruce Fischl wrote: Hi Mojdeh it won't affect any individual thickness measures, *but* will affect the estimated total intracranial volume (eTIV). We don't typically use eTIV for thickness correction, but do for things like hippocampal volume. Are you using version 5.1? If so, that's the problem. Nick has a fix for this that he can direct you about, or you can wait for 5.2 and rerun the Talairach registration then. cheers Bruce On Fri, 20 Jul 2012, Mojdeh Zamyadi wrote: Hi all, Sorry for re-posting this but it seems it didn't get through! I've just started to do cortical thickness analysis on some subjects and I'm noticing some miss-registrations, more specifically the Talairach image is smaller than the target image no matter what subject I look at! I just wanted to make sure if this is something normal and to what extend it's going to effect the individual cortical thickness calculations. I guess I'm not sure how the Talairach transformation is used in further steps of the cortical thickness calculation. I tried to attach example coronal, sagittal and horizontal slices of one of my subjects but apparently it was too big for the mailing list. Pleas let me know if there is a way to attach images here. I greatly appreciate your advice. Thanks, Mojdeh Zamyadi, MSc Clinical Research Project Assistant The Hospital for Sick Children 555 University Avenue Toronto, ON, M5G 1X8 ___ 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] cortical thickness and ICA of resting state fMRI
Hi all, I was wondering if anyone knows about any articles that compare/relate cortical thickness analysis with resting state ICA results? More specifically, I'm looking for articles that study cortical thickness changes in different regions of brain and its possible relation to group clusters found using ICA analysis of resting state fMRI. Thanks, Mojdeh Zamyadi, MSc Clinical Research Project Assistant The Hospital for Sick Children 555 University Avenue Toronto ON M5G 1X8 ___ 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.
