[Freesurfer] citation for FsFast
Hi Doug, What is your preferred citation for FsFast (used for resting-state)? I couldn't really find a clear answer in the Zotero library or mail archives. Thanks and happy holidays! Linda ___ 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] template to dicoms
Dear freesurfers, I have a bit of a strange question: does anyone know a way to write a template T1 brain (for instance fsaverage or MNI152) to dicom files? I have some very old software that only takes dicoms and it's the only software I can use to replicate previous findings, but obviously going from a template to dicoms is not that easy. I'd appreciate any tips! -- Linda Douw, Ph.D. Branco Weiss fellow Department of Radiology Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School 149 13th Street Charlestown, MA 02129 ___ 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] manual parcellation
Hi experts, I want to make a new, custom-made parcellation, based on the aparc but with much higher resolution. (I've tried mris_divide_parcellation, which yields strip-shaped instead of isometric labels, and mris_make_face_parcellation, which loses spatial specificity. The wiki describes a way of manually drawing new labels in tksurfer, but I get stuck in the process. I've created a new CLUT, with no. 100-106 being the new subdivisions of the original bankssts label: # Freesurfer LUT information extracted from annotation file: # lh.aparc.annot # 2008-02-29 23:58:32 # This file can be used as the basis for a new LUT file for annotations purposes # which can be loaded into tksurfer using File Label Load color table #No.Label Name: R G B A 0 unknown 25 525 0 1 bankssts25 10040 0 2 caudalanteriorcingulate125 100 160 0 3 caudalmiddlefrontal10025 0 0 4 corpuscallosum 1207050 0 5 cuneus 22020 100 0 6 entorhinal 2202010 0 7 fusiform 180 220 140 0 8 inferiorparietal 22060 220 0 9 inferiortemporal 18040 120 0 10 isthmuscingulate 14020 140 0 11 lateraloccipital2030 140 0 12 lateralorbitofrontal357550 0 13 lingual225 140 140 0 14 medialorbitofrontal2003575 0 15 middletemporal 160 10050 0 16 parahippocampal 20 22060 0 17 paracentral 60 22060 0 18 parsopercularis220 180 140 0 19 parsorbitalis 20 10050 0 20 parstriangularis 2206020 0 21 pericalcarine 120 10060 0 22 postcentral2202020 0 23 posteriorcingulate 220 180 220 0 24 precentral 6020 220 0 25 precuneus 160 140 180 0 26 rostralanteriorcingulate8020 140 0 27 rostralmiddlefrontal7550 125 0 28 superiorfrontal 20 220 160 0 29 superiorparietal20 180 140 0 30 superiortemporal 140 220 220 0 31 supramarginal 80 16020 0 32 frontalpole100 0 100 0 33 temporalpole707070 0 34 transversetemporal 150 150 200 0 100 bankssts_1 25 10041 0 101 bankssts_2 25 10045 0 102 bankssts_3 25 10050 0 103 bankssts_4 25 10055 0 104 bankssts_5 25 10060 0 105 bankssts_6 25 10065 0 I load the aparc and the new CLUT into tksurfer, draw points around a new label, close the path, and then custom fill the area. How do I now indicate that this is for instance the new label bankssts_1? The wiki and mailing archive indicate some problems with manually parcellating, but the info seems dated and scattered. So if there is some place I can find this stuff myself, I'd be happy to check it out. Thanks so much, -- Linda Douw, Ph.D. Research fellow ___ 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] ico4 parcellation and mri_segstats
Hi Doug, I see. I'm trying to compare fMRI to MEG, so it would be very helpful if the same parcellation (i.e. with all 2562 labels) could be used. How could I investigate why mris_make_face_parcellation skips a bunch of labels? The problem is not fsaverage5, because doing the analysis in native space of patients yield the same problem (and the same labels missing). So I guess exclusion of 102 labels always occurs in mris_make_face_parcellation? Thanks again, Linda On Mon, September 10, 2012 11:27 am, Douglas N Greve wrote: It looks like there are several (102 to be exact) that do not have any voxels in your parcellation. Eg, #82: 8282 ic4.tri_vertex_82 0 So the problem appears to be with mris_make_face_parcellation, not with mri_segstats. doug On 09/10/2012 10:56 AM, Linda Douw wrote: Hi Doug, Output and sumfile are attached. Any ideas? Linda Message: 10 Date: Mon, 13 Aug 2012 15:55:13 -0400 From: Douglas N Grevegr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Freesurfer Digest, Vol 102, Issue 10 To: freesurfer@nmr.mgh.harvard.edu Message-ID:50295ba1.8090...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed Hi Linda, can you send the terminal output for mri_segstats? Can you also send the summary file? doug On 08/13/2012 10:59 AM, Linda Douw wrote: Hi Doug, I first parcellate fsaverage5 using ico4 (all my functional data are morphed to fsaverage5 surface): mris_make_face_parcellation /fsaverage5/rh.inflated $FREESURFER_HOME/lib/bem/ic4.tri rh.ico4.annot Then I extract the waveforms using mri_segstats mri_segstats --i rh.functional.nii.gz --avgwf rh_ico4.txt --annot fsaverage5c rh ico4 --sum ico4_rh.sum Hope this clarifies the problem! Linda -- Message: 25 Date: Fri, 10 Aug 2012 11:18:38 -0400 From: Douglas N Grevegr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ico4 parcellation and mri_segstats To: freesurfer@nmr.mgh.harvard.edu Message-ID:5025264e.3030...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed what are your command lines? doug On 08/09/2012 01:21 PM, Linda Douw wrote: Dear Freesurfers, I'm trying to extract the average waveforms from all 2562 ROIs in an annotation constructed using mris_make_face_parcellation with ico4. However, I get only 2460 waveforms after doing mri_segstats, and the summary files show that several ROIs are 'skipped' for some reason. Am I missing something? Thanks, -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html -- Linda Douw, Ph.D. Research fellow Department of Radiology Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School 149 13th Street Charlestown, MA 02129 ___ 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] Freesurfer Digest, Vol 102, Issue 10
Hi Doug, I first parcellate fsaverage5 using ico4 (all my functional data are morphed to fsaverage5 surface): mris_make_face_parcellation /fsaverage5/rh.inflated $FREESURFER_HOME/lib/bem/ic4.tri rh.ico4.annot Then I extract the waveforms using mri_segstats mri_segstats --i rh.functional.nii.gz --avgwf rh_ico4.txt --annot fsaverage5c rh ico4 --sum ico4_rh.sum Hope this clarifies the problem! Linda -- Message: 25 Date: Fri, 10 Aug 2012 11:18:38 -0400 From: Douglas N Greve gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] ico4 parcellation and mri_segstats To: freesurfer@nmr.mgh.harvard.edu Message-ID: 5025264e.3030...@nmr.mgh.harvard.edu Content-Type: text/plain; charset=ISO-8859-1; format=flowed what are your command lines? doug On 08/09/2012 01:21 PM, Linda Douw wrote: Dear Freesurfers, I'm trying to extract the average waveforms from all 2562 ROIs in an annotation constructed using mris_make_face_parcellation with ico4. However, I get only 2460 waveforms after doing mri_segstats, and the summary files show that several ROIs are 'skipped' for some reason. Am I missing something? Thanks, -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html -- ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer End of Freesurfer Digest, Vol 102, Issue 10 *** ___ 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] BOLD vol2surf dimension mismatch
Hi all, I'm trying to project volume BOLD time series to native surface in some subjects. First, I registered the functional data to orig.mgz, using: bbregister --s subj --mov func.nii.gz --reg register.dat --init-fsl --bold --o output.nii.gz The results look good in tkregister2. Then, I want to go from volume to surf, doing: mri_vol2surf --mov functional.nii.gz --reg register.dat --regheader nmr00524_FS --hemi lh --o /folder/ However, it gives this error message: Done reading source surface Mapping Source Volume onto Source Subject Surface 1 0 0 0 using old Done mapping volume to surface Number of source voxels hit = 26361 Writing to /folder/ Dim: 132698 1 1 non-standard value for imnr1 (1, usually 256) in volume structure non-standard value for type (3, usually 0) in volume structure non-standard value for width (132698, usually 256) in volume structure non-standard value for height (1, usually 256) in volume structure I should probably use mri_vol2vol first, but which target volume should I then use? Or is there something else I'm doing wrong? Thanks for your help! -- Linda Douw, Ph.D. Research fellow Department of Radiology Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School 149 13th Street Charlestown, MA 02129 ___ 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] ico4 parcellation and mri_segstats
Dear Freesurfers, I'm trying to extract the average waveforms from all 2562 ROIs in an annotation constructed using mris_make_face_parcellation with ico4. However, I get only 2460 waveforms after doing mri_segstats, and the summary files show that several ROIs are 'skipped' for some reason. Am I missing something? Thanks, -- Linda Douw, Ph.D. Research fellow Department of Radiology Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School 149 13th Street Charlestown, MA 02129 ___ 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] label shape with mris_divide_parcellation
Hi Bruce, Thanks for the suggestion. I've tried mris_make_face_parcellation, but I would still prefer the parcellation being based on the original. I'm now trying to use mris_divide_parcellation in multiple steps (to try and circumvent the constraint of dividing only by the longest diameter), where I first divide aparc into a new parcellation, and then proceed dividing the new parcellation into smaller ROIs. However, this method yields very strange results, as some ROIs are and some are not divided according to textfile I've created. Do you have any idea why this is, and how to solve it? Thanks, Linda On Thu, April 19, 2012 11:08 am, Bruce Fischl wrote: Hi Linda I think that's one too many constraints. Do you need it to be based on the original parcellattion? If not and a uniform parcellation will do you can use mris_make_face_parcellation. cheers Bruce On Thu, 19 Apr 2012, Linda Douw wrote: Hi all, I would like to make a fine-grained surface parcellation from aparc - let's say 500 labels, and I would like the labels to be more or less isometric. When subdividing the parcellation with mris_divide_parcellation, the labels become very stretched instead of isometric. Is there a way to get a different result? Thanks! -- Linda Douw, Ph.D. Research fellow Department of Radiology Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School 149 13th Street Charlestown, MA 02129 ___ 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] label shape with mris_divide_parcellation
Hi all, I would like to make a fine-grained surface parcellation from aparc - let's say 500 labels, and I would like the labels to be more or less isometric. When subdividing the parcellation with mris_divide_parcellation, the labels become very stretched instead of isometric. Is there a way to get a different result? Thanks! -- Linda Douw, Ph.D. Research fellow Department of Radiology Athinoula A. Martinos Center for Biomedical Imaging Massachusetts General Hospital Harvard Medical School 149 13th Street Charlestown, MA 02129 ___ 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] custom making an overlay
Hi freesurfers, Is it possible to make an overlay to load into tksurfer containing any type of data (for instance, centrality measures computed with graph theory) for a particular annotation? In the mailing archive, I've found tips about creating a custom LUT table and making it a segmentation, but you need the coordinates of the labels for that. In my case, I've made my own parcellation by using mris_divide_parcellation, so then I would have to know where to find the coordinates (I don't). And do you think this is the most efficient method? Thanks! -- Linda Douw, Ph.D. ___ 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] dimensions of input and annot for mri_segstats
Hi all, I have nifti files containing the surface-projected time series data of a subject (obtained using procsurffast), both lh and rh. These time series are projected onto fsaverage5, and are 3414 x 1 x 3 time points, where 3414*3 = 10242 are the number of vertices for each hemisphere. Now, I would like to extract the mean time series for 138 ROIs, which are defined in an annotation called sparc I made: mris_divide_parcellation fsaverage5 lh aparc.annot sparc.txt lh.sparc I would assume that these files are now of the same dimensions. However, when I run: mri_segstats --i /subject/surf/subject_projectedto_fsaverage5.nii.gz --avgwf /subject1/ts_lh.txt --annot fsaverage5 lh sparc it crashes because the dimensions are not the same (the segmentation is 10242 x 1 x 1). They do both overlay nicely on fsaverage5 inflated using tksurfer. What may cause this mismatch? And is there a solution? Thanks, Linda ___ 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] label transformation to MNI space
Hi Doug, Thanks for the reply. This cmd makes it slightly better I guess, but still definetely off target. It seems to be shift downward, towards inferior, and therefore sometimes outside the skull. Any other ideas? Linda The way the reg is set up, the targ is your mask. Try this cmd: mri_vol2vol --targ lh_entorhinal.nii.gz --mov MNI152_T1_2mm.brain.nii.gz --o lh_entorhinal_MNI.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat --inv doug Linda Douw wrote: Hi all, I am trying to transform some labels from the aparc to masks in MNI space. Ideally, I would like to do this for each subject in my study individually (using their own rawavg.mgz and labels), but for now I started out with fsaverage. I first converted the label file into a nifti: mri_label2vol --label ./fsaverage/label/lh.entorhinal.label --subject fsaverage --temp ./fsaverage/mri/brainmask.mgz --o lh_entorhinal.nii.gz --identity And then put the nifti file containing the label into MNI space: mri_vol2vol --mov lh_entorhinal.nii.gz --targ MNI152_T1_2mm.brain.nii.gz --o lh_entorhinal_MNI.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat But when I open lh_entorhinal_MNI.nii.gz with fslview, the location is completely wrong. I checked the location with tkregister as well: tkregister2 --mov lh_entorhinal_MNI.nii.gz --reg /$FREESURFER_HOME/average/mni152.register.dat But here the entorhinal was also in the wrong place. Do you know how to fix this? Thanks, -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html -- Linda Douw, PhD. ___ 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] label transformation to MNI space
This fixed the problem, thanks! The problem appears to be with the label itself. Try this conversion: mri_label2label --srclabel lh.entorhinal.label --s fsaverage --regmethod surface --trglabel lh.entorhinal.new.label --hemi lh Also, you might want to use the entorhinal label define in the aparc+aseg since it fills in the ribbon: mri_binarize --i aparc+aseg.mgz --match 1006 --o lh_entorhinal.nii.gz 1006 comes from $FREESURFER_HOME/FreeSurferColorLUT.txt doug Linda Douw wrote: Hi Doug, Thanks for the reply. This cmd makes it slightly better I guess, but still definetely off target. It seems to be shift downward, towards inferior, and therefore sometimes outside the skull. Any other ideas? Linda The way the reg is set up, the targ is your mask. Try this cmd: mri_vol2vol --targ lh_entorhinal.nii.gz --mov MNI152_T1_2mm.brain.nii.gz --o lh_entorhinal_MNI.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat --inv doug Linda Douw wrote: Hi all, I am trying to transform some labels from the aparc to masks in MNI space. Ideally, I would like to do this for each subject in my study individually (using their own rawavg.mgz and labels), but for now I started out with fsaverage. I first converted the label file into a nifti: mri_label2vol --label ./fsaverage/label/lh.entorhinal.label --subject fsaverage --temp ./fsaverage/mri/brainmask.mgz --o lh_entorhinal.nii.gz --identity And then put the nifti file containing the label into MNI space: mri_vol2vol --mov lh_entorhinal.nii.gz --targ MNI152_T1_2mm.brain.nii.gz --o lh_entorhinal_MNI.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat But when I open lh_entorhinal_MNI.nii.gz with fslview, the location is completely wrong. I checked the location with tkregister as well: tkregister2 --mov lh_entorhinal_MNI.nii.gz --reg /$FREESURFER_HOME/average/mni152.register.dat But here the entorhinal was also in the wrong place. Do you know how to fix this? Thanks, -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: www.nmr.mgh.harvard.edu/facility/filedrop/index.html -- Linda Douw, PhD. ___ 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] label transformation to MNI space
Hi all, I am trying to transform some labels from the aparc to masks in MNI space. Ideally, I would like to do this for each subject in my study individually (using their own rawavg.mgz and labels), but for now I started out with fsaverage. I first converted the label file into a nifti: mri_label2vol --label ./fsaverage/label/lh.entorhinal.label --subject fsaverage --temp ./fsaverage/mri/brainmask.mgz --o lh_entorhinal.nii.gz --identity And then put the nifti file containing the label into MNI space: mri_vol2vol --mov lh_entorhinal.nii.gz --targ MNI152_T1_2mm.brain.nii.gz --o lh_entorhinal_MNI.nii.gz --reg $FREESURFER_HOME/average/mni152.register.dat But when I open lh_entorhinal_MNI.nii.gz with fslview, the location is completely wrong. I checked the location with tkregister as well: tkregister2 --mov lh_entorhinal_MNI.nii.gz --reg /$FREESURFER_HOME/average/mni152.register.dat But here the entorhinal was also in the wrong place. Do you know how to fix this? Thanks, -- Linda Douw, PhD. ___ 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.
