Re: [Freesurfer] mri_vol2surf --projopt
Sorry for this question, but now I am confused. Do you mean that I should not use projopt and just use the interpolation? If so why should I not use projfrac? On Tue, 08 Apr 2014 15:02:36 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: You'll have to do without it for now and just do the interpolation On 04/08/2014 03:32 AM, Joerg Pfannmoeller wrote: Well, I need to use that option. In this case I will just interpolate to the 1 mm grid and proceed this way. On Mon, 07 Apr 2014 12:14:47 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Sorry, I don't understand. You mean it still segfaults without --projopt or that you have to use projopt? On 04/07/2014 02:36 AM, Joerg Pfannmoeller wrote: Unfortunately that is no option for me. On Fri, 04 Apr 2014 15:33:47 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Don't use --projopt and it won't segfault On 04/03/2014 02:08 AM, Joerg Pfannmoeller wrote: The command is: mri_vol2surf --mov /.../f001.nii --reg /.../register.f1.dof6.dat --trgsubject subjid --interp nearest --projopt /.../map001 --hemi rh --o /.../f001_surf.nii --noreshape --cortex The output is the follwoing: srcvol = /.../f001.nii srcreg = /.../register.f001.dof6.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = subjid surfreg = sphere.reg reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Loading label /.../label/rh.cortex.label Reading surface /.../surf/rh.white Done reading source surface Reading thickness /.../surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface reading gm volume fraction from /.../map001.gm.mgz reading wm volume fraction from /.../map001.wm.mgz reading csf volume fraction from /.../map001.csf.mgz mri_vol2surf --mov /.../f001.nii --reg /.../register.f1.dof6.dat --trgsubject subjid --interp nearest --projopt /.../map001 --hemi rh --o /.../f001_surf.nii --noreshape --cortex: Segmentation fault Do you have an idea about the cause of the error? On Wed, 02 Apr 2014 17:28:14 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: what is your command line that is seg faulting? What is the terminal output? On 04/02/2014 05:17 PM, pfannmo...@uni-greifswald.de wrote: Please help me with this issue: If I apply mri_surf2vol to a single volume of unprocessed epi-data, it results in a segmentation fault. It works if I apply mri_vol2vol for registration of epi and anatomy, but than an interpolation is involved. I would like to avoid the interpolation and apply mri_surf2vol directly to the unprocessed data in order to minimize the number of interpolations. At Wednesday, 02-04-2014 on 21:08 Douglas N Greve wrote: This is something BF added Sept 1 2009: added --projopt switch to do optimal linear estimation of gray matter values given a set of precomputed gray matter densities. I don't know what it would mean beyond that doug On 04/02/2014 10:49 AM, Joerg Pfannmoeller wrote: Hello, I found an option in mri_vol2surf for which I could not find a documentation. The option is called: --projopt It would be nice if somebody could give a description of this option. Respectfully yours pfannmoe ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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
Re: [Freesurfer] mri_surcluster and centroid option
On Mon, 07 Apr 2014 12:02:24 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Is this group data? Or otherwise on fsaverage? Or on the subject's surface? It is on a single subject on its on anatomy (self). How are you determining that the centroid is outside of the cluster? The coordinates are outside the cluster, there is nothing to worry about that. It should give you a vertex number for the centroid (I think). As you told in your last mail it gives Tal-coordinates and not vertices. I opted not to use the centroid by default for this reason. This can happen because the centroid is irregular. I don not understand this: What do you mean by irregular? ___ 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] longitudinal template generation with manual registration
Dear Experts, i am analyzing a longitudinal study (three timepoints for each participant). I manually register the second and third timepoint to the first timepoint using freeview. Question: Is it possible to use these manually created transformation matrices to create a common template that is equidistant from all three timepoints to balance interpolation ? If so, which commands do I need to use ? (As I understand mri_robust_template does this, but I would like to use manual rather than automatic registration.) Many thanks in advance! Andreas ___ 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] Problem of size
Hi FreeSurfer expert,I have a problem with command recon-all. In recon-all.log I can read:«The physical sizes are (256.00 mm, 256.00 mm, 312.00 mm), which cannot fit in 256^3 mm^3 volume.The resulting volume will have 312 slices.If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu).»I hope are there anyone to help me.Thank for your help.Andrea ___ 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] Questions about byvoxel statistics from Tracula
Hello I'm using Tracula to analyse our DWI-images. Freesurfer reconstructions of the corresponding T1-images have been perfomed before. Respectively, the version used are 1.53 and 5.3. The Tracula process works fine and I have extracted the statistics for all tracts. About this statistics, I wanted to know what is the difference between FA and FA_Avg ? An other question about the values extracted is about the coordinates in the file byvoxel.txt. Are they correspind with the coordinates of the voxel in the dtifit image were the values were extracted? The last question, can we extracted the same by tract statistics from an other image like a PET registered to the DWI with your code? Thanks for your answer -- Emilie Poirion Master 1 Informatique Industrielle et Imagerie Industrielle Université Pierre et Marie Curie (Paris 6) ___ 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] Intermediate stages of cortical inflation
you can use -w 1 to write out every step in the inflation process and choose what you want. If you want it to preserve surface area during inflation (as opposed to just at the end), also include -scale 1 cheers Bruce On Wed, 9 Apr 2014, Xuelong Zhao wrote: Hi, I would like to ask whether it is possible to display different levels of cortical inflation? I have been using the command: mris_inflate but the -dist and -n flags do not seem to make that much difference. Also, if I use fsaverage lh.orig as the input file and using the default options for mris_Inflate I don't seem to be able to recover the lh.inflated surface. Are there any alternative commands to control the level of inflation? Thanks. ___ 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] mri_surcluster and centroid option
Hi Jeorg if the cluster is non-convex, the centroid is not guaranteed to be in the interior. Think of a C or U shape. cheers Bruce On Wed, 9 Apr 2014, Joerg Pfannmoeller wrote: On Mon, 07 Apr 2014 12:02:24 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Is this group data? Or otherwise on fsaverage? Or on the subject's surface? It is on a single subject on its on anatomy (self). How are you determining that the centroid is outside of the cluster? The coordinates are outside the cluster, there is nothing to worry about that. It should give you a vertex number for the centroid (I think). As you told in your last mail it gives Tal-coordinates and not vertices. I opted not to use the centroid by default for this reason. This can happen because the centroid is irregular. I don not understand this: What do you mean by irregular? ___ 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] Problem of size
Hi Andrea what size are your voxels? Do you really need an FOV that big? If not, you could extract the central 256mm using mri_extract. And I believe this is just a warning - does recon-all complete? cheers Bruce On Wed, 9 Apr 2014, Andrea Tateo wrote: Hi FreeSurfer expert, I have a problem with command recon-all. In recon-all.log I can read: «The physical sizes are (256.00 mm, 256.00 mm, 312.00 mm), which cannot fit in 256^3 mm^3 volume. The resulting volume will have 312 slices. If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu).» I hope are there anyone to help me. Thank for your help. Andrea ___ 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] mri_vol2surf --projopt
You can use --projfrac (which can perform an interpolation with --interp trilinear) On 4/9/14 2:44 AM, Joerg Pfannmoeller wrote: Sorry for this question, but now I am confused. Do you mean that I should not use projopt and just use the interpolation? If so why should I not use projfrac? On Tue, 08 Apr 2014 15:02:36 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: You'll have to do without it for now and just do the interpolation On 04/08/2014 03:32 AM, Joerg Pfannmoeller wrote: Well, I need to use that option. In this case I will just interpolate to the 1 mm grid and proceed this way. On Mon, 07 Apr 2014 12:14:47 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Sorry, I don't understand. You mean it still segfaults without --projopt or that you have to use projopt? On 04/07/2014 02:36 AM, Joerg Pfannmoeller wrote: Unfortunately that is no option for me. On Fri, 04 Apr 2014 15:33:47 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Don't use --projopt and it won't segfault On 04/03/2014 02:08 AM, Joerg Pfannmoeller wrote: The command is: mri_vol2surf --mov /.../f001.nii --reg /.../register.f1.dof6.dat --trgsubject subjid --interp nearest --projopt /.../map001 --hemi rh --o /.../f001_surf.nii --noreshape --cortex The output is the follwoing: srcvol = /.../f001.nii srcreg = /.../register.f001.dof6.dat srcregold = 0 srcwarp unspecified surf = white hemi = rh trgsubject = subjid surfreg = sphere.reg reshape = 0 interp = nearest float2int = round GetProjMax = 0 INFO: float2int code = 0 INFO: changing type to float Done loading volume Loading label /.../label/rh.cortex.label Reading surface /.../surf/rh.white Done reading source surface Reading thickness /.../surf/rh.thickness Done Mapping Source Volume onto Source Subject Surface reading gm volume fraction from /.../map001.gm.mgz reading wm volume fraction from /.../map001.wm.mgz reading csf volume fraction from /.../map001.csf.mgz mri_vol2surf --mov /.../f001.nii --reg /.../register.f1.dof6.dat --trgsubject subjid --interp nearest --projopt /.../map001 --hemi rh --o /.../f001_surf.nii --noreshape --cortex: Segmentation fault Do you have an idea about the cause of the error? On Wed, 02 Apr 2014 17:28:14 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: what is your command line that is seg faulting? What is the terminal output? On 04/02/2014 05:17 PM, pfannmo...@uni-greifswald.de wrote: Please help me with this issue: If I apply mri_surf2vol to a single volume of unprocessed epi-data, it results in a segmentation fault. It works if I apply mri_vol2vol for registration of epi and anatomy, but than an interpolation is involved. I would like to avoid the interpolation and apply mri_surf2vol directly to the unprocessed data in order to minimize the number of interpolations. At Wednesday, 02-04-2014 on 21:08 Douglas N Greve wrote: This is something BF added Sept 1 2009: added --projopt switch to do optimal linear estimation of gray matter values given a set of precomputed gray matter densities. I don't know what it would mean beyond that doug On 04/02/2014 10:49 AM, Joerg Pfannmoeller wrote: Hello, I found an option in mri_vol2surf for which I could not find a documentation. The option is called: --projopt It would be nice if somebody could give a description of this option. Respectfully yours pfannmoe ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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
Re: [Freesurfer] mri_surcluster and centroid option
By irregular, I mean irregularly shaped (non-concave) such that the centroid is actually not inside the cluster. Eg, a ring would have the centroid in the center but technically it would not be in the ring On 4/9/14 2:48 AM, Joerg Pfannmoeller wrote: On Mon, 07 Apr 2014 12:02:24 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Is this group data? Or otherwise on fsaverage? Or on the subject's surface? It is on a single subject on its on anatomy (self). How are you determining that the centroid is outside of the cluster? The coordinates are outside the cluster, there is nothing to worry about that. It should give you a vertex number for the centroid (I think). As you told in your last mail it gives Tal-coordinates and not vertices. I opted not to use the centroid by default for this reason. This can happen because the centroid is irregular. I don not understand this: What do you mean by irregular? ___ 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] Fwd: Freesurfer QDEC Buckner Data
Saurabh, Every instance I can recall in which someone on the list has posted an issue with downloading freesurfer (or freesurfer data) the issue was due to something on the users ends. Most often the problem is due to file size limits on clients networks. In every case the problem was solved by using another network. I have tested the link and it is working properly. Please try downloading the data from a network other than the one that is giving you problems. -Zeke On 04/09/2014 01:30 AM, Saurabh Thakur wrote: Hello Freesurfer Expert, I am not able to download the Bucker_data-tutorial_subjs completely. Downloading is stopped after 2.5 Gb. I am looking for *quick reply* to download the data set. PFA the screen short of terminal window. Thanks in advance. cheers Saurabh Thakur, -- Forwarded message -- From: *Saurabh Thakur* srbht...@gmail.com mailto:srbht...@gmail.com Date: Tue, Apr 8, 2014 at 8:57 AM Subject: Re: [Freesurfer] Freesurfer QDEC Buckner Data To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu mailto:freesurfer@nmr.mgh.harvard.edu Hello Freesurfer expert, PFA screen short of the terminal. It is happening every time i try to download. Please suggest some alternative to download the buckner_tutorial_data_subjs. Thanks in advance, cheers Saurabh Thakur, On Tue, Apr 8, 2014 at 12:00 AM, Saurabh Thakur srbht...@gmail.com mailto:srbht...@gmail.com wrote: Hi Louis, I have been trying to download using Linux as well as windows but after 3.3GB , link is getting disconnected. Once i even reached 99.9% download using FTP file but package is not getting opened neither getting 100% download complete. Do you have any other alternative mirror link to download the file wgetftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.tar.gz -c thanks in advance cheers Saurabh Thakur, On Mon, Apr 7, 2014 at 9:42 PM, Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu mailto:vi...@nmr.mgh.harvard.edu wrote: Hi Saurabh, Did the wget command fail for you? I just tried it and the download started without any issues. You can also just paste the ftp address into your browser and download it that way as well. -Louis On Mon, 7 Apr 2014, Saurabh Thakur wrote: Hello Freesurfer Expert, I am working on QDEC and looking forward to download buckner_data from link mentioned below: wget ftp://surfer.nmr.mgh.harvard.edu/pub/data/buckner_data-tutorial_subjs.tar.gz Needing data asap. Please share alternative mirror link to download the buckner_data. cheers Saurabh Thakur, ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto: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 mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] mri_surcluster and centroid option
Hi, I am sorry to disappoint you. I wrote another srcipt to compute the centroid in order to clarify whats happening. The centroid computed by the script is in the center of the cluster. However, the differences could be due to details of the computation. I was not able to unriddle all the details in the freesurfer code. Probably I am going to keep this script since it fits what I would like to compute. Before I forget about it, I use freesurfer 5.3. Greetings pfannmoe On Wed, 9 Apr 2014 08:33:26 -0400 (EDT) Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Jeorg if the cluster is non-convex, the centroid is not guaranteed to be in the interior. Think of a C or U shape. cheers Bruce On Wed, 9 Apr 2014, Joerg Pfannmoeller wrote: On Mon, 07 Apr 2014 12:02:24 -0400 Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Is this group data? Or otherwise on fsaverage? Or on the subject's surface? It is on a single subject on its on anatomy (self). How are you determining that the centroid is outside of the cluster? The coordinates are outside the cluster, there is nothing to worry about that. It should give you a vertex number for the centroid (I think). As you told in your last mail it gives Tal-coordinates and not vertices. I opted not to use the centroid by default for this reason. This can happen because the centroid is irregular. I don not understand this: What do you mean by irregular? ___ 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] mris_divide_parcellation same divisions between subjects
In the mri_extract_label, there is a label number. Where would I find this
for the new labels?
i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz 2035
${subj_dir}/hardi_labels/ctx-rh-insula.nii
On Tue, Apr 8, 2014 at 10:50 PM, Douglas Greve gr...@nmr.mgh.harvard.eduwrote:
yep, exactly
On 4/8/14 6:00 PM, Corinna Bauer wrote:
Hi Doug,
After I have the labels then in each subject's T1 space, I will need to
then put them into diffusion and resting state space.
I already have scripts that put the parcellations into subject-specific
diffusion/resting state space (using bbregister, tkregister2, mri_vol2vol
(using the inverse registration from bbregister to put the T1 into
diffusion space), mri_extract_label (extract labels from aparc+aseg.mgz),
and then mri_label2vol (register each of the extracted labels into
diffusion space). Would a similar approach work for the new labels?
Corinna
On Tue, Apr 8, 2014 at 5:42 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:
Exactly what you have described won't work very well because it would be
in the volume. I would divide up the parcellations in fsaverage space
like you've done, then map the parcellation to each subject using
mri_surf2surf (--sval-annot, see example 6)
doug
On 04/08/2014 04:54 PM, Corinna Bauer wrote:
Hello all,
I am planning to use mris_divide_parcellation to split the Desikan
atlas into smaller ROIs, but will need the new ROIs to be consistent
between subjects.
Can I achieve this if I register each subject to fsaverage space and
then apply the inverse transform to the divided parcellations (which
are currently done on the fsaverage brain)?
If so, for extracting each label, what would be used for the label
number?
(i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz *2035*
${subj_dir}/hardi_labels/ctx-rh-insula.nii)
Thanks
Corinna
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gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358
Fax: 617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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e-mail
contains patient information, please contact the Partners Compliance
HelpLine at
http://www.partners.org/complianceline . If the e-mail was sent to you
in error
but does not contain patient information, please contact the sender and
properly
dispose of the e-mail.
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Re: [Freesurfer] mris_divide_parcellation same divisions between subjects
$FREESURFER_HOME/FreeSurferColorLUT.txt
cheers
Bruce
On Wed, 9 Apr 2014, Corinna Bauer
wrote:
In the mri_extract_label, there is a label number. Where would I find this
for the new labels?
i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz 2035
${subj_dir}/hardi_labels/ctx-rh-insula.nii
On Tue, Apr 8, 2014 at 10:50 PM, Douglas Greve gr...@nmr.mgh.harvard.edu
wrote:
yep, exactly
On 4/8/14 6:00 PM, Corinna Bauer wrote:
Hi Doug,
After I have the labels then in each subject's T1 space, I
will need to then put them into diffusion and resting
state space.
I already have scripts that put the parcellations into
subject-specific diffusion/resting state space (using
bbregister, tkregister2, mri_vol2vol (using the inverse
registration from bbregister to put the T1 into diffusion
space), mri_extract_label (extract labels from
aparc+aseg.mgz), and then mri_label2vol (register each of
the extracted labels into diffusion space). Would a
similar approach work for the new labels?
Corinna
On Tue, Apr 8, 2014 at 5:42 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:
Exactly what you have described won't work very well
because it would be
in the volume. I would divide up the parcellations
in fsaverage space
like you've done, then map the parcellation to each
subject using
mri_surf2surf (--sval-annot, see example 6)
doug
On 04/08/2014 04:54 PM, Corinna Bauer wrote:
Hello all,
I am planning to use mris_divide_parcellation to
split the Desikan
atlas into smaller ROIs, but will need the new
ROIs to be consistent
between subjects.
Can I achieve this if I register each subject to
fsaverage space and
then apply the inverse transform to the divided
parcellations (which
are currently done on the fsaverage brain)?
If so, for extracting each label, what would be
used for the label
number?
(i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz
*2035*
${subj_dir}/hardi_labels/ctx-rh-insula.nii)
Thanks
Corinna
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--
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: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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Re: [Freesurfer] mris_divide_parcellation same divisions between subjects
It looks like the FreeSurferColorLUT.txt does not contain the label number
for the newly created labels (divided from the desikan atlas).
On Wed, Apr 9, 2014 at 9:53 AM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote:
$FREESURFER_HOME/FreeSurferColorLUT.txt
cheers
Bruce
On Wed, 9 Apr 2014, Corinna Bauer
wrote:
In the mri_extract_label, there is a label number. Where would I find
this
for the new labels?
i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz 2035
${subj_dir}/hardi_labels/ctx-rh-insula.nii
On Tue, Apr 8, 2014 at 10:50 PM, Douglas Greve
gr...@nmr.mgh.harvard.edu
wrote:
yep, exactly
On 4/8/14 6:00 PM, Corinna Bauer wrote:
Hi Doug,
After I have the labels then in each subject's T1 space, I
will need to then put them into diffusion and resting
state space.
I already have scripts that put the parcellations into
subject-specific diffusion/resting state space (using
bbregister, tkregister2, mri_vol2vol (using the inverse
registration from bbregister to put the T1 into diffusion
space), mri_extract_label (extract labels from
aparc+aseg.mgz), and then mri_label2vol (register each of
the extracted labels into diffusion space). Would a
similar approach work for the new labels?
Corinna
On Tue, Apr 8, 2014 at 5:42 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:
Exactly what you have described won't work very well
because it would be
in the volume. I would divide up the parcellations
in fsaverage space
like you've done, then map the parcellation to each
subject using
mri_surf2surf (--sval-annot, see example 6)
doug
On 04/08/2014 04:54 PM, Corinna Bauer wrote:
Hello all,
I am planning to use mris_divide_parcellation to
split the Desikan
atlas into smaller ROIs, but will need the new
ROIs to be consistent
between subjects.
Can I achieve this if I register each subject to
fsaverage space and
then apply the inverse transform to the divided
parcellations (which
are currently done on the fsaverage brain)?
If so, for extracting each label, what would be
used for the label
number?
(i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz
*2035*
${subj_dir}/hardi_labels/ctx-rh-insula.nii)
Thanks
Corinna
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--
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: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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contains patient information, please contact the Partners
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sent to you in error
but does not contain patient information, please contact
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dispose of the e-mail.
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Re: [Freesurfer] mris_divide_parcellation same divisions between subjects
Should I make up my own LUT for the new ROIs that specifies some colour and
label number?
On Wed, Apr 9, 2014 at 10:00 AM, Corinna Bauer corinna...@gmail.com wrote:
It looks like the FreeSurferColorLUT.txt does not contain the label number
for the newly created labels (divided from the desikan atlas).
On Wed, Apr 9, 2014 at 9:53 AM, Bruce Fischl
fis...@nmr.mgh.harvard.eduwrote:
$FREESURFER_HOME/FreeSurferColorLUT.txt
cheers
Bruce
On Wed, 9 Apr 2014, Corinna Bauer
wrote:
In the mri_extract_label, there is a label number. Where would I find
this
for the new labels?
i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz 2035
${subj_dir}/hardi_labels/ctx-rh-insula.nii
On Tue, Apr 8, 2014 at 10:50 PM, Douglas Greve
gr...@nmr.mgh.harvard.edu
wrote:
yep, exactly
On 4/8/14 6:00 PM, Corinna Bauer wrote:
Hi Doug,
After I have the labels then in each subject's T1 space, I
will need to then put them into diffusion and resting
state space.
I already have scripts that put the parcellations into
subject-specific diffusion/resting state space (using
bbregister, tkregister2, mri_vol2vol (using the inverse
registration from bbregister to put the T1 into diffusion
space), mri_extract_label (extract labels from
aparc+aseg.mgz), and then mri_label2vol (register each of
the extracted labels into diffusion space). Would a
similar approach work for the new labels?
Corinna
On Tue, Apr 8, 2014 at 5:42 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:
Exactly what you have described won't work very well
because it would be
in the volume. I would divide up the parcellations
in fsaverage space
like you've done, then map the parcellation to each
subject using
mri_surf2surf (--sval-annot, see example 6)
doug
On 04/08/2014 04:54 PM, Corinna Bauer wrote:
Hello all,
I am planning to use mris_divide_parcellation to
split the Desikan
atlas into smaller ROIs, but will need the new
ROIs to be consistent
between subjects.
Can I achieve this if I register each subject to
fsaverage space and
then apply the inverse transform to the divided
parcellations (which
are currently done on the fsaverage brain)?
If so, for extracting each label, what would be
used for the label
number?
(i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz
*2035*
${subj_dir}/hardi_labels/ctx-rh-insula.nii)
Thanks
Corinna
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--
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: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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contains patient information, please contact the Partners
Compliance HelpLine at
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sent to you in error
but does not contain patient information, please contact
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Re: [Freesurfer] mris_divide_parcellation same divisions between subjects
oh, those should be embedded in the .annot file it creates
On Wed, 9 Apr
2014, Corinna Bauer wrote:
It looks like the FreeSurferColorLUT.txt does not contain the label number
for the newly created labels (divided from the desikan atlas).
On Wed, Apr 9, 2014 at 9:53 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu
wrote:
$FREESURFER_HOME/FreeSurferColorLUT.txt
cheers
Bruce
On Wed, 9 Apr 2014, Corinna Bauer
wrote:
In the mri_extract_label, there is a label number. Where would
I find this
for the new labels?
i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz 2035
${subj_dir}/hardi_labels/ctx-rh-insula.nii
On Tue, Apr 8, 2014 at 10:50 PM, Douglas Greve
gr...@nmr.mgh.harvard.edu
wrote:
yep, exactly
On 4/8/14 6:00 PM, Corinna Bauer wrote:
Hi Doug,
After I have the labels then in each subject's T1 space,
I
will need to then put them into diffusion and resting
state space.
I already have scripts that put the parcellations into
subject-specific diffusion/resting state space (using
bbregister, tkregister2, mri_vol2vol (using the inverse
registration from bbregister to put the T1 into
diffusion
space), mri_extract_label (extract labels from
aparc+aseg.mgz), and then mri_label2vol (register each
of
the extracted labels into diffusion space). Would a
similar approach work for the new labels?
Corinna
On Tue, Apr 8, 2014 at 5:42 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:
Exactly what you have described won't work very well
because it would be
in the volume. I would divide up the parcellations
in fsaverage space
like you've done, then map the parcellation to each
subject using
mri_surf2surf (--sval-annot, see example 6)
doug
On 04/08/2014 04:54 PM, Corinna Bauer wrote:
Hello all,
I am planning to use mris_divide_parcellation to
split the Desikan
atlas into smaller ROIs, but will need the new
ROIs to be consistent
between subjects.
Can I achieve this if I register each subject to
fsaverage space and
then apply the inverse transform to the divided
parcellations (which
are currently done on the fsaverage brain)?
If so, for extracting each label, what would be
used for the label
number?
(i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz
*2035*
${subj_dir}/hardi_labels/ctx-rh-insula.nii)
Thanks
Corinna
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--
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: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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contains patient information, please contact the Partners
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Re: [Freesurfer] mris_divide_parcellation same divisions between subjects
you'll need to figure it out from the volume itself by loading the seg
with both -seg and -aux. When you find the label you want, click on it
and the aux value in the control window will tell you what the id is
doug
On 04/09/2014 09:41 AM, Corinna Bauer wrote:
In the mri_extract_label, there is a label number. Where would I find
this for the new labels?
i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz 2035
${subj_dir}/hardi_labels/ctx-rh-insula.nii
On Tue, Apr 8, 2014 at 10:50 PM, Douglas Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:
yep, exactly
On 4/8/14 6:00 PM, Corinna Bauer wrote:
Hi Doug,
After I have the labels then in each subject's T1 space, I will
need to then put them into diffusion and resting state space.
I already have scripts that put the parcellations into
subject-specific diffusion/resting state space (using bbregister,
tkregister2, mri_vol2vol (using the inverse registration from
bbregister to put the T1 into diffusion space), mri_extract_label
(extract labels from aparc+aseg.mgz), and then mri_label2vol
(register each of the extracted labels into diffusion space).
Would a similar approach work for the new labels?
Corinna
On Tue, Apr 8, 2014 at 5:42 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:
Exactly what you have described won't work very well because
it would be
in the volume. I would divide up the parcellations in
fsaverage space
like you've done, then map the parcellation to each subject using
mri_surf2surf (--sval-annot, see example 6)
doug
On 04/08/2014 04:54 PM, Corinna Bauer wrote:
Hello all,
I am planning to use mris_divide_parcellation to split the
Desikan
atlas into smaller ROIs, but will need the new ROIs to be
consistent
between subjects.
Can I achieve this if I register each subject to fsaverage
space and
then apply the inverse transform to the divided
parcellations (which
are currently done on the fsaverage brain)?
If so, for extracting each label, what would be used for
the label
number?
(i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz *2035*
${subj_dir}/hardi_labels/ctx-rh-insula.nii)
Thanks
Corinna
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--
Douglas N. Greve, Ph.D.
MGH-NMR Center
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
Phone Number: 617-724-2358 tel:617-724-2358
Fax: 617-726-7422 tel:617-726-7422
Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting
FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2
www.nmr.mgh.harvard.edu/facility/filedrop/index.html
http://www.nmr.mgh.harvard.edu/facility/filedrop/index.html
Outgoing:
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/
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sent to you in error
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Re: [Freesurfer] mris_divide_parcellation same divisions between subjects
Perfect. Thanks!
On Wed, Apr 9, 2014 at 10:22 AM, Douglas N Greve
gr...@nmr.mgh.harvard.eduwrote:
you'll need to figure it out from the volume itself by loading the seg
with both -seg and -aux. When you find the label you want, click on it
and the aux value in the control window will tell you what the id is
doug
On 04/09/2014 09:41 AM, Corinna Bauer wrote:
In the mri_extract_label, there is a label number. Where would I find
this for the new labels?
i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz 2035
${subj_dir}/hardi_labels/ctx-rh-insula.nii
On Tue, Apr 8, 2014 at 10:50 PM, Douglas Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:
yep, exactly
On 4/8/14 6:00 PM, Corinna Bauer wrote:
Hi Doug,
After I have the labels then in each subject's T1 space, I will
need to then put them into diffusion and resting state space.
I already have scripts that put the parcellations into
subject-specific diffusion/resting state space (using bbregister,
tkregister2, mri_vol2vol (using the inverse registration from
bbregister to put the T1 into diffusion space), mri_extract_label
(extract labels from aparc+aseg.mgz), and then mri_label2vol
(register each of the extracted labels into diffusion space).
Would a similar approach work for the new labels?
Corinna
On Tue, Apr 8, 2014 at 5:42 PM, Douglas N Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
wrote:
Exactly what you have described won't work very well because
it would be
in the volume. I would divide up the parcellations in
fsaverage space
like you've done, then map the parcellation to each subject
using
mri_surf2surf (--sval-annot, see example 6)
doug
On 04/08/2014 04:54 PM, Corinna Bauer wrote:
Hello all,
I am planning to use mris_divide_parcellation to split the
Desikan
atlas into smaller ROIs, but will need the new ROIs to be
consistent
between subjects.
Can I achieve this if I register each subject to fsaverage
space and
then apply the inverse transform to the divided
parcellations (which
are currently done on the fsaverage brain)?
If so, for extracting each label, what would be used for
the label
number?
(i.e. mri_extract_label ${subj_dir}/mri/aparc+aseg.mgz *2035*
${subj_dir}/hardi_labels/ctx-rh-insula.nii)
Thanks
Corinna
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[Freesurfer] R: Re: Problem of size
Hi Bruce, thanks for the quick response. I report the full error message: WARNING =====The physical sizes are (256.00 mm, 256.00 mm, 312.00 mm), which cannot fit in 256^3 mm^3 volume.The resulting volume will have 312 slices.If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu).===== $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $reading from /lustre/home/tateo/Simulazione_FREESURF_GRID_2/Segmentazione/SUB_1006_3/001/mri/rawavg.mgz...TR=0.00, TE=0.00, TI=0.00, flip angle=0.00i_ras = (-1, 0, -0)j_ras = (0, 0, -1)k_ras = (-0, 1, -0)Original Data has (1, 1, 1) mm size and (256, 256, 312) voxels.Data is conformed to 1 mm size and 312 voxels for all directionschanging data type from float to uchar (noscale = 0)...MRIchangeType: Building histogramReslicing using trilinear interpolationwriting to /lustre/home/tateo/Simulazione_FREESURF_GRID_2/Segmentazione/SUB_1006_3/001/mri/orig.mgz... ERROR! FOV=312.000 256Include the flag -cw256 with recon-all! Thank you very much Andrea Messaggio originale Da: fis...@nmr.mgh.harvard.edu Data: 9-apr-2014 14.45 A: Andrea Tateoandrea.ta...@virgilio.it, Freesurfer support listfreesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] Problem of size Hi Andrea what size are your voxels? Do you really need an FOV that big? If not, you could extract the central 256mm using mri_extract. And I believe this is just a warning - does recon-all complete? cheers Bruce On Wed, 9 Apr 2014, Andrea Tateo wrote: Hi FreeSurfer expert, I have a problem with command recon-all. In recon-all.log I can read: «The physical sizes are (256.00 mm, 256.00 mm, 312.00 mm), which cannot fit in 256^3 mm^3 volume. The resulting volume will have 312 slices. If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu).» I hope are there anyone to help me. Thank for your help. Andrea 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] R: Re: Problem of size
Hi Andrea will it fit in 256? You can try specifying -cw256 cheers Bruce On Wed, 9 Apr 2014, Andrea Tateo wrote: Hi Bruce, thanks for the quick response. I report the full error message: WARNING=== == The physical sizes are (256.00 mm, 256.00 mm, 312.00 mm), which cannot fit in 256^3 mm^3 volume. The resulting volume will have 312 slices. If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu). === == $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from/lustre/home/tateo/Simulazione_FREESURF_GRID_2/Segmentazione/SUB_1006_3/001 /mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, -0) j_ras = (0, 0, -1) k_ras = (-0, 1, -0) Original Data has (1, 1, 1) mm size and (256, 256, 312) voxels. Data is conformed to 1 mm size and 312 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to/lustre/home/tateo/Simulazione_FREESURF_GRID_2/Segmentazione/SUB_1006_3/001 /mri/orig.mgz... ERROR! FOV=312.000 256 Include the flag -cw256 with recon-all! Thank you very much Andrea Messaggio originale Da: fis...@nmr.mgh.harvard.edu Data: 9-apr-2014 14.45 A: Andrea Tateoandrea.ta...@virgilio.it, Freesurfer support listfreesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] Problem of size Hi Andrea what size are your voxels? Do you really need an FOV that big? If not, you could extract the central 256mm using mri_extract. And I believe this is just a warning - does recon-all complete? cheers Bruce On Wed, 9 Apr 2014, Andrea Tateo wrote: Hi FreeSurfer expert, I have a problem with command recon-all. In recon-all.log I can read: «The physical sizes are (256.00 mm, 256.00 mm, 312.00 mm), which cannot fit in 256^3 mm^3 volume. The resulting volume will have 312 slices. If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu).» I hope are there anyone to help me. Thank for your help. Andrea 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] R: Re: R: Re: Problem of size
I use « recon-all -debug -s 001 -autorecon-all» and after « mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o 001_rawavg.mgz --regheader aseg.mgz » Where can I specify-cw256 ? Messaggio originale Da: fis...@nmr.mgh.harvard.edu Data: 9-apr-2014 16.56 A: Andrea Tateoandrea.ta...@virgilio.it Cc: Freesurfer support listfreesurfer@nmr.mgh.harvard.edu Ogg: Re: R: Re: [Freesurfer] Problem of size Hi Andrea will it fit in 256? You can try specifying -cw256 cheers Bruce On Wed, 9 Apr 2014, Andrea Tateo wrote: Hi Bruce, thanks for the quick response. I report the full error message: WARNING=== == The physical sizes are (256.00 mm, 256.00 mm, 312.00 mm), which cannot fit in 256^3 mm^3 volume. The resulting volume will have 312 slices. If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu). === == $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ reading from/lustre/home/tateo/Simulazione_FREESURF_GRID_2/Segmentazione/SUB_1006_3/001 /mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, -0) j_ras = (0, 0, -1) k_ras = (-0, 1, -0) Original Data has (1, 1, 1) mm size and (256, 256, 312) voxels. Data is conformed to 1 mm size and 312 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writing to/lustre/home/tateo/Simulazione_FREESURF_GRID_2/Segmentazione/SUB_1006_3/001 /mri/orig.mgz... ERROR! FOV=312.000 256 Include the flag -cw256 with recon-all! Thank you very much Andrea Messaggio originale Da: fis...@nmr.mgh.harvard.edu Data: 9-apr-2014 14.45 A: Andrea Tateoandrea.ta...@virgilio.it, Freesurfer support listfreesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] Problem of size Hi Andrea what size are your voxels? Do you really need an FOV that big? If not, you could extract the central 256mm using mri_extract. And I believe this is just a warning - does recon-all complete? cheers Bruce On Wed, 9 Apr 2014, Andrea Tateo wrote: Hi FreeSurfer expert, I have a problem with command recon-all. In recon-all.log I can read: «The physical sizes are (256.00 mm, 256.00 mm, 312.00 mm), which cannot fit in 256^3 mm^3 volume. The resulting volume will have 312 slices. If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu).» I hope are there anyone to help me. Thank for your help. Andrea 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] R: Re: R: Re: Problem of size
on the recon-all command line On Wed, 9 Apr 2014, Andrea Tateo wrote: I use « recon-all -debug -s 001 -autorecon-all » and after « mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o 001_rawavg.mgz --regheader aseg.mgz » Where can I specify -cw256 ? Messaggio originale Da: fis...@nmr.mgh.harvard.edu Data: 9-apr-2014 16.56 A: Andrea Tateoandrea.ta...@virgilio.it Cc: Freesurfer support listfreesurfer@nmr.mgh.harvard.edu Ogg: Re: R: Re: [Freesurfer] Problem of size Hi Andrea will it fit in 256? You can try specifying -cw256 cheers Bruce On Wed, 9 Apr 2014, Andrea Tateo wrote: Hi Bruce, thanks for the quick response. I report the full error message: WARNING==== === == The physical sizes are (256.00 mm, 256.00 mm, 312.00 mm), which cannot fit in 256^3 mm^3 volume. The resulting volume will have 312 slices. If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu). === == $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ readingfrom/lustre/home/tateo/Simulazione_FREESURF_GRID_2/Segmentazione/SUB_1006_3 /001 /mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, -0) j_ras = (0, 0, -1) k_ras = (-0, 1, -0) Original Data has (1, 1, 1) mm size and (256, 256, 312) voxels. Data is conformed to 1 mm size and 312 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writingto/lustre/home/tateo/Simulazione_FREESURF_GRID_2/Segmentazione/SUB_1006_3/0 01 /mri/orig.mgz... ERROR! FOV=312.000 256 Include the flag -cw256 with recon-all! Thank you very much Andrea Messaggio originale Da: fis...@nmr.mgh.harvard.edu Data: 9-apr-2014 14.45 A: Andrea Tateoandrea.ta...@virgilio.it, Freesurfer support listfreesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] Problem of size Hi Andrea what size are your voxels? Do you really need an FOV that big? If not, you could extract the central 256mm using mri_extract. And I believe this is just a warning - does recon-all complete? cheers Bruce On Wed, 9 Apr 2014, Andrea Tateo wrote: Hi FreeSurfer expert, I have a problem with command recon-all. In recon-all.log I can read: «The physical sizes are (256.00 mm, 256.00 mm, 312.00 mm), which cannot fit in 256^3 mm^3 volume. The resulting volume will have 312 slices. If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu).» I hope are there anyone to help me. Thank for your help. Andrea 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] R: Re: R: Re: R: Re: Problem of size
Endless thanks. I'll try and update you. Andrea Messaggio originale Da: fis...@nmr.mgh.harvard.edu Data: 9-apr-2014 17.16 A: Andrea Tateoandrea.ta...@virgilio.it Cc: Freesurfer support listfreesurfer@nmr.mgh.harvard.edu Ogg: Re: R: Re: R: Re: [Freesurfer] Problem of size on the recon-all command line On Wed, 9 Apr 2014, Andrea Tateo wrote: I use « recon-all -debug -s 001 -autorecon-all» and after « mri_label2vol --seg aseg.mgz --temp rawavg.mgz --o 001_rawavg.mgz --regheader aseg.mgz » Where can I specify-cw256 ? Messaggio originale Da: fis...@nmr.mgh.harvard.edu Data: 9-apr-2014 16.56 A: Andrea Tateoandrea.ta...@virgilio.it Cc: Freesurfer support listfreesurfer@nmr.mgh.harvard.edu Ogg: Re: R: Re: [Freesurfer] Problem of size Hi Andrea will it fit in 256? You can try specifying -cw256 cheers Bruce On Wed, 9 Apr 2014, Andrea Tateo wrote: Hi Bruce, thanks for the quick response. I report the full error message: WARNING==== === == The physical sizes are (256.00 mm, 256.00 mm, 312.00 mm), which cannot fit in 256^3 mm^3 volume. The resulting volume will have 312 slices. If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu). === == $Id: mri_convert.c,v 1.179.2.2 2011/05/16 20:53:47 greve Exp $ readingfrom/lustre/home/tateo/Simulazione_FREESURF_GRID_2/Segmentazione/SUB_1006_3 /001 /mri/rawavg.mgz... TR=0.00, TE=0.00, TI=0.00, flip angle=0.00 i_ras = (-1, 0, -0) j_ras = (0, 0, -1) k_ras = (-0, 1, -0) Original Data has (1, 1, 1) mm size and (256, 256, 312) voxels. Data is conformed to 1 mm size and 312 voxels for all directions changing data type from float to uchar (noscale = 0)... MRIchangeType: Building histogram Reslicing using trilinear interpolation writingto/lustre/home/tateo/Simulazione_FREESURF_GRID_2/Segmentazione/SUB_1006_3/0 01 /mri/orig.mgz... ERROR! FOV=312.000 256 Include the flag -cw256 with recon-all! Thank you very much Andrea Messaggio originale Da: fis...@nmr.mgh.harvard.edu Data: 9-apr-2014 14.45 A: Andrea Tateoandrea.ta...@virgilio.it, Freesurfer support listfreesurfer@nmr.mgh.harvard.edu Ogg: Re: [Freesurfer] Problem of size Hi Andrea what size are your voxels? Do you really need an FOV that big? If not, you could extract the central 256mm using mri_extract. And I believe this is just a warning - does recon-all complete? cheers Bruce On Wed, 9 Apr 2014, Andrea Tateo wrote: Hi FreeSurfer expert, I have a problem with command recon-all. In recon-all.log I can read: «The physical sizes are (256.00 mm, 256.00 mm, 312.00 mm), which cannot fit in 256^3 mm^3 volume. The resulting volume will have 312 slices. If you find problems, please let us know (freesurfer@nmr.mgh.harvard.edu).» I hope are there anyone to help me. Thank for your help. Andrea 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] read cluster summary into Matlab?
Hi! I was wondering whether there is code available to quickly read cluster summary files into Matlab? I need access to the cluster-wise p-values. Thank you very much! Caspar ___ 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] read cluster summary into Matlab?
no, sorry On 04/09/2014 01:18 PM, Caspar M. Schwiedrzik wrote: Hi! I was wondering whether there is code available to quickly read cluster summary files into Matlab? I need access to the cluster-wise p-values. Thank you very much! Caspar ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ 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] Two positions (post-doc and software engineer) in Marseille, France
Title: signatureMail2011 Dear all, we have two positions opening in Marseille, France, for the study and modelling of brain development. Descriptions can be found at the following URLs: https://dl.dropboxusercontent.com/u/3372764/EngineerPosition_lefevreMarseille.pdf https://dl.dropboxusercontent.com/u/3372764/PostDocPosition_lefevreMarseille2.pdf If interested, pease contact Dr Julien Lefvre at: julien.lefe...@univ-amu.fr Olivier -- Olivier Coulon,CNRS research Fellow, olivier.cou...@univ-amu.fr Tel: +33491828527fax: +33491828550 http://olivier.coulon.perso.esil.univmed.fr LSIS Laboratory, IM TeamESIL, Campus de Luminy, Case 925, 13288 Marseille cedex 09, FRANCE http://www.lsis.org/brainmorph ___ 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] basic high res data question
Good afternoon gurus- I’m new to FS and working with 0.7mm iso 7T MPRAGEs. After bias-correction with AFNI’s 3dUnifize, recon-all ran without hitch but downsampled everything to 1mm. Now I have basically the same sentiment and question as this thread from ~2 years ago (i’m linking to the middle for simplicity): http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg22852.html What’s the very latest on this? Thanks! -Salvatore (Sam) Torrisi Section on the Neurobiology of Fear and Anxiety National Institute of Mental Health ___ 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] basic high res data question
Hello all, I have a related question as I am also a freesurfer beginner and starting to use it on submilliter MP2RAGE 7T images. After having had a quick look at the videos, tutos and the archives, I found this: http://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon BTW on that page I guess that the line: recon-all -mprage -normalization -skulstrip -s $SUBJ should read recon-all -mprage -normalization *-skullstrip* -s $SUBJ For a test run and to familiarize mysef with freesurfer and the trouble shooting steps, I ran the basic recon-all on one of the native images which gave me results at a 1 mm res. My question is: is there any reason why these steps should work differently for a MP2RAGE compared to the MPRAGE described the HiResRecon page? For testing, I am currently running the steps in the page mentioned above on one image for practice before running more subjects. So far, so good but the following command: mri_nu_correct.mni --i $SUBJECTS_DIR/$SUBJ/mri/orig.mgz --o $SUBJECTS_DIR/$SUBJ/mri/nu.mgz --proto-iters 1000 --distance 15 --fwhm 0.15 --n 1 --uchar $SUBJECTS_DIR/$SUBJ/mri/transforms/talairach.xfm issued the following warning: Use of ?PATTERN? without explicit operator is deprecated at ~/Program/freesurfer/mni/bin/sharpen_volume line 153. Thanks *Remi Gau * On 09/04/14 21:57, Torrisi, Sam (NIH/NIMH) [F] wrote: Good afternoon gurus- I’m new to FS and working with 0.7mm iso 7T MPRAGEs. After bias-correction with AFNI’s 3dUnifize, recon-all ran without hitch but downsampled everything to 1mm. Now I have basically the same sentiment and question as this thread from ~2 years ago (i’m linking to the middle for simplicity): http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg22852.html What’s the very latest on this? Thanks! -Salvatore (Sam) Torrisi Section on the Neurobiology of Fear and Anxiety National Institute of Mental Health ___ 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] Freeview, fsaverage_sym aparc.annot
Hi Freesurfer experts, I'm trying to view aparc.annot on a fsaverage_sym surface. I can load aparc.a2009a.annot with freeview -f $SUBJECTS_DIR/fsaverage_sym/surf/lh.pial:annot=aparc.a2009s.annot but attempting freeview -f $SUBJECTS_DIR/fsaverage_sym/surf/lh.pial:annot=aparc.annot results in freeview crashing. The command window output is in the attached text file. (Freeview 1.0 May 14, 2013; Mac OS 10.9.2) Thanks, Peggy $ freeview -f $SUBJECTS_DIR/fsaverage_sym/surf/lh.pial:annot=aparc.annot 2014-04-09 17:40:44.789 Freeview[2054:303] invalid drawable 2014-04-09 17:40:44.790 Freeview[2054:303] invalid drawable 2014-04-09 17:40:44.801 Freeview[2054:303] invalid drawable 2014-04-09 17:40:44.802 Freeview[2054:303] invalid drawable 2014-04-09 17:40:44.812 Freeview[2054:303] invalid drawable 2014-04-09 17:40:44.813 Freeview[2054:303] invalid drawable 2014-04-09 17:40:44.824 Freeview[2054:303] invalid drawable 2014-04-09 17:40:44.824 Freeview[2054:303] invalid drawable Did not find any volume geometry information in the surface pÌ|ÿreading colortable from annotation file... colortable with 1036 entries read (originally /scratch/tmpdir.annot2std.28231/seg.1.073.xhemi.ctab) [0]PETSC ERROR: [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: - Error Message [0]PETSC ERROR: Signal received! [0]PETSC ERROR: [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See docs/changes/index.html for recent updates. [0]PETSC ERROR: See docs/faq.html for hints about trouble shooting. [0]PETSC ERROR: See docs/index.html for manual pages. [0]PETSC ERROR: [0]PETSC ERROR: Unknown Name on a darwin12. named LoanWolf by peggy Wed Apr 9 17:40:43 2014 [0]PETSC ERROR: Libraries linked from /usr/pubsw/packages/petsc/2.3.3-p13-64b/src/petsc-2.3.3-p13/lib/darwin12.2.0-c-opt [0]PETSC ERROR: Configure run at Mon Dec 17 15:29:35 2012 [0]PETSC ERROR: Configure options --with-debugging=no --with-cc=gcc --with-fc=0 --download-f-blas-lapack=0 --download-mpich=1 --with-mpi=1 --with-x=0 --with-gnu-copyright-code=0 --with-shared=0 COPTFLAGS=-O3 CXXOPTFLAGS=-O3 FOPTFLAGS=-O3 [0]PETSC ERROR: [0]PETSC ERROR: User provided function() line 0 in unknown directory unknown file [unset]: aborting job: application called MPI_Abort(MPI_COMM_WORLD, 59) - process 0 $ freeview -f $SUBJECTS_DIR/fsaverage_sym/surf/lh.pial:annot=aparc.annot 2014-04-09 17:40:44.789 Freeview[2054:303] invalid drawable 2014-04-09 17:40:44.790 Freeview[2054:303] invalid drawable 2014-04-09 17:40:44.801 Freeview[2054:303] invalid drawable 2014-04-09 17:40:44.802 Freeview[2054:303] invalid drawable 2014-04-09 17:40:44.812 Freeview[2054:303] invalid drawable 2014-04-09 17:40:44.813 Freeview[2054:303] invalid drawable 2014-04-09 17:40:44.824 Freeview[2054:303] invalid drawable 2014-04-09 17:40:44.824 Freeview[2054:303] invalid drawable Did not find any volume geometry information in the surface pÌ|ÿreading colortable from annotation file... colortable with 1036 entries read (originally /scratch/tmpdir.annot2std.28231/seg.1.073.xhemi.ctab) [0]PETSC ERROR: [0]PETSC ERROR: Caught signal number 11 SEGV: Segmentation Violation, probably memory access out of range [0]PETSC ERROR: Try option -start_in_debugger or -on_error_attach_debugger [0]PETSC ERROR: or see http://www.mcs.anl.gov/petsc/petsc-as/documentation/troubleshooting.html#Signal[0]PETSC ERROR: or try http://valgrind.org on linux or man libgmalloc on Apple to find memory corruption errors [0]PETSC ERROR: configure using --with-debugging=yes, recompile, link, and run [0]PETSC ERROR: to get more information on the crash. [0]PETSC ERROR: - Error Message [0]PETSC ERROR: Signal received! [0]PETSC ERROR: [0]PETSC ERROR: Petsc Release Version 2.3.3, Patch 13, Thu May 15 17:29:26 CDT 2008 HG revision: 4466c6289a0922df26e20626fd4a0b4dd03c8124 [0]PETSC ERROR: See
[Freesurfer] select_talairach_point function?
Hi I am sorry if my question is really basic, but I am choosing the seeds for fsfast resting state connectivity analysis, and I am looking at the different options in the litterature. Seeds are often presented with the talairach coordinates, and I was looking for a way to find the corresponding vertex number on fsaverage surface, so that I can build the corresponding label that I could use for the fcseed-sess command. I found this previous email, and there seem to be a command to do that but I don't know how to launch this command select_talairach_point xtal ytal ztal Thank you very much Celine -Message d'origine- De : Bruce Fischl [mailto:fischl at nmr.mgh.harvard.edu] Envoyé : mercredi, 10. février 2010 16:18 À : Ben Hamida Cammoun Leila Faiza Cc : freesurfer at nmr.mgh.harvard.edu Objet : Re: [Freesurfer] ROI based on Talairach coordinate Hi Leila, you can use the tcl command select_talairach_point xtal ytal ztal in tksurfer in the tcl window (with the % prompt), then make a label from that point and dilate it a few times. cheers, Bruce On Wed, 10 Feb 2010, Ben Hamida Cammoun Leila Faiza wrote: Dear Freesurfer users and experts, This is my second attempt :( I am trying to construct a roi based on some talairach coordinate coming from a paper, but I completely fail to do it with matlab and neither manually with tksurfer. My first try was to use the transformation Talairach.xfm with matlab, inverse it and try to recover RAS coordinate, it gives me completely wrong values. Second try was to introduce the Tal coordinate directly in Tksurfer, which is not possible I think (correct me if I am wrong), with the version I have the is a bug in tkmedit I guess when introducing Talairach coord (the ideas was to save them and to load the vertex in tksurfer).. the values changes in the edit box.. Is there another way?? Is it possible with script? Or how to do this by matlab? Please don't ignore the request. Leila ___ 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 about byvoxel statistics from Tracula
Bonsoir Emilie - Tracula draws a large number of path samples, which in the end are added up to produce the path probability distribution. FA shows the values of FA at each point along the path sample with the greatest probability, i.e., along a single 1D curve. FA_Avg averages the FA from all the path samples at corresponding points along their trajectory. Because it is an average of many values rather than a single value, FA_Avg will tend to be less noisy and more reliable. Currently there is no way to average other values along the path, but you can trick the software into doing it. Find the dmri_pathstats command line corresponding to the tract that you want in trac-all.log. Rename dmri/dtifit_FA.nii.gz to something else temporarily, and rename the volume that you want to get values along the tract from as dmri/dtifit_FA.nii.gz. Now when you run the same dmri_pathstats command, the pathstats.byvoxel.txt file will contain the values from the new volume in the FA/FA_Avg columns, instead of the values from the FA volume. The coordinates in the stats files are in the subject's native DWI space. Hope this helps, a.y PS: For combining the pathstats.byvoxel.txt files across subjects, get the latest tracula update, if you haven't: http://surfer.nmr.mgh.harvard.edu/fswiki/Tracula/#Updates On Wed, 9 Apr 2014, Emilie Poirion wrote: Hello I'm using Tracula to analyse our DWI-images. Freesurfer reconstructions of the corresponding T1-images have been perfomed before. Respectively, the version used are 1.53 and 5.3. The Tracula process works fine and I have extracted the statistics for all tracts. About this statistics, I wanted to know what is the difference between FA and FA_Avg ? An other question about the values extracted is about the coordinates in the file byvoxel.txt. Are they correspind with the coordinates of the voxel in the dtifit image were the values were extracted? The last question, can we extracted the same by tract statistics from an other image like a PET registered to the DWI with your code? Thanks for your answer -- Emilie Poirion Master 1 Informatique Industrielle et Imagerie Industrielle Université Pierre et Marie Curie (Paris 6) ___ 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] Create a label from a binary mask
Hello, Sorry for the late reply. It ended up working and overlapping correctly in freeview. Thank you On Friday, April 4, 2014 4:30 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: Try this first mri_cor2label --c aseg.mgz --id 17 --l lh.hippo.label Then load lh.hippo.label If wramygdala.R.001.nii is not in the conformed space, your command will not work On 04/04/2014 05:17 PM, Cherisse Onuigbo wrote: mri_cor2label --c wramygdala.R.001.nii --id 1 --l wramygdala.R.001.label tkmedit Subjects_for_Cherisse/S001 T1.mgz -aux brainmask.mgz -seg aseg.mgz And then I added the label using the drop down menu. On Friday, April 4, 2014 3:45 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu wrote: What were your mri_cor2label and tkmedit command lines? SPM will never work properly for what you are trying to do. On 04/04/2014 04:42 PM, Cherisse Onuigbo wrote: I first checked it in tkmedit, but I didn't see the region in green as I went through the slices. I also put another label in there just to check if I was displaying labels correctly and others showed up. Then I used the display function in spm and input the coordinates there, but it showed that the coordinates were outside the region. Also I was wondering why in the label file, all of the vertex id's are -1 instead of what I specify in the command. On Friday, April 4, 2014 3:08 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: How are you checking the vertex coordinates? You can't use SPM, you'll have to use tkmedit or freeview On 04/04/2014 04:04 PM, Cherisse Onuigbo wrote: My mask is a volume mask. When I run the function normally, the vertices that are in the text file do not fall in the region of my mask. On Friday, April 4, 2014 2:28 PM, Douglas N Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Hi Cherisse, i don't understand what you have done. Is the mask a volume mask or surface mask? In mri_cor2label, you can specify a surface to get surface vertex numbers. doug On 04/02/2014 07:03 PM, Cherisse Onuigbo wrote: Hello I was wondering how to create a label from a binary mask. I created a mask and then normalized it to the template space. When I tried to use mri_cor2vol, all the vertex numbers come out as -1. I understand that the vertex numbers should come out as -1, but when I entered the coordinates in the display function in spm, it was not in the region. Thank you, Cherisse ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D. MGH-NMR Center gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu Phone Number: 617-724-2358 Fax: 617-726-7422 Bugs: surfer.nmr.mgh.harvard.edu/fswiki/BugReporting FileDrop: https://gate.nmr.mgh.harvard.edu/filedrop2 www.nmr.mgh.harvard.edu/facility/filedrop/index.html Outgoing: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto: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 mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer -- Douglas N. Greve, Ph.D.
Re: [Freesurfer] Freeview, fsaverage_sym aparc.annot
It appears to have the same issue on Linux as well. Thanks for the feedback. We will look into it. Ruopeng On Apr 9, 2014, at 5:53 PM, Peggy Skelly peggy.ske...@gmail.com wrote: Hi Freesurfer experts, I'm trying to view aparc.annot on a fsaverage_sym surface. I can load aparc.a2009a.annot with freeview -f $SUBJECTS_DIR/fsaverage_sym/surf/lh.pial:annot=aparc.a2009s.annot but attempting freeview -f $SUBJECTS_DIR/fsaverage_sym/surf/lh.pial:annot=aparc.annot results in freeview crashing. The command window output is in the attached text file. (Freeview 1.0 May 14, 2013; Mac OS 10.9.2) Thanks, Peggy error.txterror.txt___ 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] fsaverage mesh has duplicate pt
Hi, I loaded the lh.orig cortex for fsaverage into Matlab. My colleague and I found that it actually has a duplicate point. The index of the duplicate points are: 1 40970 I checked that both have the same vertices coordinates: -36.7233 -18.4039 64.3611 I'm not sure if this is intentional or not but wanted to draw the freesurfer community's attention to this in case it is a bug. Also, I believe a similar issue is present for fsaverage's lh.pial and rh.orig (I haven't checked other cortices). Regards, AZ ___ 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] fsaverage mesh has duplicate pt
Can confirm also true for lh.white, but not lh.sphere and lh.inflated. --Thomas On Thu, Apr 10, 2014 at 1:11 PM, Xuelong Zhao andrewz...@live.com.au wrote: Hi, I loaded the lh.orig cortex for fsaverage into Matlab. My colleague and I found that it actually has a duplicate point. The index of the duplicate points are: 1 40970 I checked that both have the same vertices coordinates: -36.7233 -18.4039 64.3611 I'm not sure if this is intentional or not but wanted to draw the freesurfer community's attention to this in case it is a bug. Also, I believe a similar issue is present for fsaverage's lh.pial and rh.orig (I haven't checked other cortices). Regards, AZ ___ 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
