Re: [Freesurfer] how to convert fsaverage space mask into other subject original space
Hi Bruce and others, I completed the mri_annotation2label and mri_label2label(which used mask created from the mri_binarize), but the result is the same as that without mask.Here are my codes: mri_binarize --i *.ocn.mgh --match 1 --o cluster1.mgh mri_annotation2label --subject fsaverage --hemi rh --outdir $SUBJECTS_DIR/fsaverage/label mri_label2label --srclabel $SUBJECTS_DIR/fsaverage/label/rh.superiofrontal.label --srcsubject fsaverage --trgsubject test --regmethod volume --srcmask cluster1.mgh 1 bfloat Last step used the mask, but its result is just tha same as that without mask. I also checked the mask file which doesnot have any problem. Thanks. All the best. Rujing Zha At 2014-04-08 23:10:35,Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: what kind of a mask? If a label you can use mri_label2label cheers Bruce On Tue, 8 Apr 2014, Rujing Zha wrote: Hi FS experts and others, I try to check my group analysis result by seeing the subjects' original space corresponding area. So I need to know how to convert my mask from fsaverage space into specific subject's space. Thanks All the best. RujingZha ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Mac OSX installations incomplete? What to do?
Thank you Zeke, that seems to work all fine! Best, Markus 2014-04-08 21:17 GMT+02:00 Z K zkauf...@nmr.mgh.harvard.edu: Markus, Thanks for pointing that out. I have added those files to the ftp link. -Zeke On 04/04/2014 04:16 PM, Markus Gschwind wrote: Thank you Zeke, What about these? /usr/local/freesurfer/bin/bet.fsl /usr/local/freesurfer/bin/flirt.fsl /usr/local/freesurfer/bin/slicetimer.fsl They are not there neither compared to the ubuntu install. Best, Markus 2014-04-04 19:05 GMT+02:00 Z K zkauf...@nmr.mgh.harvard.edu mailto:zkauf...@nmr.mgh.harvard.edu: There are 3 missing fsl files from the OSX snow leopard installation. They can be downloaded from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/zkaufman/fsl Copy them into your $FREESURFER_HOME/bin directory. -Zeke On 04/04/2014 12:32 PM, Markus Gschwind wrote: Dear Freesurfers, As discovered here, http://www.mail-archive.com/freesurfer@nmr.mgh.harvard. edu/msg35160.html it seams that some Mac OSX installations suffered from incomplete files. I just veryfied that I had downloaded the complete image and wget says yes: Logging in as anonymous ... Logged in! == SYST ... done.== PWD ... done. == TYPE I ... done. == CWD (1) /pub/dist/freesurfer/5.3.0 ... done. == SIZE freesurfer-Darwin-snowleopard- i686-stable-pub-v5.3.0.dmg ... 3394499614 File has already been retrieved. 2014-04-04 18:24:26 (0.00 B/s) - 'freesurfer-Darwin-snowleopard-i686-stable-pub-v5.3.0.dmg' saved [3394499614] So this is what I installed recently and it seems that there are some files missing (at least some of the fsl-functions in bin). Doug, you said that you suspected that it could be a problem of the installer script? What should we do (also Eiran) in order to complete the installation? Thanks for you work! Markus ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu mailto:Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer ___ 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 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
Allright! The only point I would like to emphasize is: Regardless if option trilin or nearest is used I need to interpolate the functional data to the structural image of the subject. This might be due to a feature of the function build_sample_array in the mri_vol2surf source code. In this function there are some constant values (din = 1.0, dout = 0.1, nsamples = 10), which might be the reason why I need to interpolate the functional data to the structural image. Currently I can not investigate the code any further. Do you have enough experience with the source code to clarify this question? On Wed, 09 Apr 2014 09:31:57 -0400 Douglas Greve gr...@nmr.mgh.harvard.edu wrote: 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
Re: [Freesurfer] basic high res data question
When running this : recon-all -maskbfs -segmentation -fill -tessellate -s $SUBJECT_HighRes mentionned on this page: http://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon I get these : mri_tessellate: max vertices 100 exceeded recon-all -s Subject_12 exited with ERRORS at Thu Apr 10 11:16:42 BST 2014 Seems the issue has been raised before in this thread: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg31331.html So I have a similar request: would it be possible to provide another compiled version of mri_tessellate (centos6_x86_64-stable-pub-5.3.0) with the an increased max number of faces and vertices? Sorry to be so needy. Thanks in advance Remi Gau ___ 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
Is it also possible to track the inflation all the way to the sphere? I was hoping that I could take snapshots of equi-area intermediate forms as the cortex is unfolded onto the sphere instead of stopping at the inflated cortex. Thanks. Date: Wed, 9 Apr 2014 08:31:46 -0400 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu CC: gr...@nmr.mgh.harvard.edu Subject: 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. ___ 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] caudate and putamen to surface
Dear all, I want to use caudate and putamen as seed in surface to do PROBTRACK in FSL. For doing that, I acquired target surface which in the cortex seed using kris_convert and label2surf script. But I met some problems in extracting caudate and putamen in the surface. At first I used mdi_extract_label sub1/mri/aseg.auto.noCCseg.mgz 11 /test/L_Caudate.mgz” and it generated L_Caudate.mgz correctly. And then in order to do mri_vol2surf I did bbregister used “bbregister —s sub1 —mov sub1/mri/brain —init-fsl —reg sub1/mri/register.dat”. Then “mdi_vol2surf —src /test/L_Caudate.mgz —srcreg sub1/mri/register.dat —promfrac 0.5 —hemi lh —out /test/L_Caudate2surf.mgz”. Everything looked like went well by the time. But it’s weird when “mri_binarize —i /test/L_Caudate2surf.mgz —min 0.5 —o /test/L_Caudate2surf_bin.mgz” , it showed “Dound 0 values in range” and “Found 0 voxels in final mask”. I checked /test/L_Caudate.mgz and found it was correct. I am wondering is that because of register.dat which I am not very clear how to acquire it correctly? Or is that because lh.white was default used in mri_vol2surf? Could you give me any advises to work around this program? And may be about how to acquire register.dat in this context and how to transform this kind of ROI to surface. Thanks a lot! Sincerely, Jinnan ___ 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] mris_divide_parcellation same divisions between subjects
For creating corresponding wm segmentations to the rois derived from
mris_divide_parcellation, should mri_aparc2wmseg be used or should I follow
the steps outlined in this posting
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-February/013471.html?
Thanks
Corinna
On Wed, Apr 9, 2014 at 10:28 AM, Corinna Bauer corinna...@gmail.com wrote:
Perfect. Thanks!
On Wed, Apr 9, 2014 at 10:22 AM, Douglas N Greve
gr...@nmr.mgh.harvard.edu wrote:
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
___
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 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/
___
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 mailto:
Freesurfer@nmr.mgh.harvard.edu
Re: [Freesurfer] mris_divide_parcellation same divisions between subjects
Use mri_aparc2aseg with the --labelwm option. Look in the recon-all.log
file for an example command line that generates wmparc.mgz
doug
On 04/10/2014 09:52 AM, Corinna Bauer wrote:
For creating corresponding wm segmentations to the rois derived from
mris_divide_parcellation, should mri_aparc2wmseg be used or should I
follow the steps outlined in this posting
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-February/013471.html
?
Thanks
Corinna
On Wed, Apr 9, 2014 at 10:28 AM, Corinna Bauer corinna...@gmail.com
mailto:corinna...@gmail.com wrote:
Perfect. Thanks!
On Wed, Apr 9, 2014 at 10:22 AM, Douglas N Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:
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
mailto: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
mailto: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
___
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.
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
Re: [Freesurfer] mris_divide_parcellation same divisions between subjects
Hi Doug,
Following the example in recon-all.log, I tried this: mri_aparc2aseg --s
FGH_09112013 --labelwm --hypo-as-wm --rip-unknown --volmask --o
mri/wmdivided.mgz --annot aparc.split
and received and mgh Write error.mghWrite(mri/wmdivided.mgz, -1): could not
open file
On Thu, Apr 10, 2014 at 11:11 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:
Use mri_aparc2aseg with the --labelwm option. Look in the recon-all.log
file for an example command line that generates wmparc.mgz
doug
On 04/10/2014 09:52 AM, Corinna Bauer wrote:
For creating corresponding wm segmentations to the rois derived from
mris_divide_parcellation, should mri_aparc2wmseg be used or should I
follow the steps outlined in this posting
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-February/013471.html
?
Thanks
Corinna
On Wed, Apr 9, 2014 at 10:28 AM, Corinna Bauer corinna...@gmail.com
mailto:corinna...@gmail.com wrote:
Perfect. Thanks!
On Wed, Apr 9, 2014 at 10:22 AM, Douglas N Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu
wrote:
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
mailto: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
mailto: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
___
Freesurfer mailing list
Freesurfer@nmr.mgh.harvard.edu
Re: [Freesurfer] how to convert fsaverage space mask into other subject original space
Please send the terminal output for mri_label2label On 04/10/2014 02:16 AM, Rujing Zha wrote: Hi Bruce and others, I completed the mri_annotation2label and mri_label2label(which used mask created from the mri_binarize), but the result is the same as that without mask.Here are my codes: mri_binarize --i *.ocn.mgh --match 1 --o cluster1.mgh mri_annotation2label --subject fsaverage --hemi rh --outdir $SUBJECTS_DIR/fsaverage/label mri_label2label --srclabel $SUBJECTS_DIR/fsaverage/label/rh.superiofrontal.label --srcsubject fsaverage --trgsubject test --regmethod volume --srcmask cluster1.mgh 1 bfloat Last step used the mask, but its result is just tha same as that without mask. I also checked the mask file which doesnot have any problem. Thanks. All the best. Rujing Zha At 2014-04-08 23:10:35,Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: what kind of a mask? If a label you can use mri_label2label cheers Bruce On Tue, 8 Apr 2014, Rujing Zha wrote: Hi FS experts and others, I try to check my group analysis result by seeing the subjects' original space corresponding area. So I need to know how to convert my mask from fsaverage space into specific subject's space. Thanks All the best. RujingZha ___ 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 -- 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
Re: [Freesurfer] mri_vol2surf --projopt
I don't understand what the question is. If you need to interpolate, then use --interp trilinear doug On 04/10/2014 04:36 AM, Joerg Pfannmoeller wrote: Allright! The only point I would like to emphasize is: Regardless if option trilin or nearest is used I need to interpolate the functional data to the structural image of the subject. This might be due to a feature of the function build_sample_array in the mri_vol2surf source code. In this function there are some constant values (din = 1.0, dout = 0.1, nsamples = 10), which might be the reason why I need to interpolate the functional data to the structural image. Currently I can not investigate the code any further. Do you have enough experience with the source code to clarify this question? On Wed, 09 Apr 2014 09:31:57 -0400 Douglas Greve gr...@nmr.mgh.harvard.edu wrote: 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
Re: [Freesurfer] basic high res data question
Hi Remi I believe I upped that limit by an order of magnitude, which hopefully would be enough? If so, Zeke can get you a new version cheers Bruce On Thu, 10 Apr 2014, Remi Gau wrote: When running this : recon-all -maskbfs -segmentation -fill -tessellate -s $SUBJECT_HighRes mentionned on this page: http://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon I get these : mri_tessellate: max vertices 100 exceeded recon-all -s Subject_12 exited with ERRORS at Thu Apr 10 11:16:42 BST 2014 Seems the issue has been raised before in this thread: http://www.mail-archive.com/freesurfer%40nmr.mgh.harvard.edu/msg31331.html So I have a similar request: would it be possible to provide another compiled version of mri_tessellate (centos6_x86_64-stable-pub-5.3.0) with the an increased max number of faces and vertices? Sorry to be so needy. Thanks in advance Remi Gau ___ 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] Intermediate stages of cortical inflation
yes, many of our binaries take the -w n flag to write out a snapshot of the minimization every nth step, including mris_sphere cheers Bruce On Thu, 10 Apr 2014, Xuelong Zhao wrote: Is it also possible to track the inflation all the way to the sphere? I was hoping that I could take snapshots of equi-area intermediate forms as the cortex is unfolded onto the sphere instead of stopping at the inflated cortex. Thanks. Date: Wed, 9 Apr 2014 08:31:46 -0400 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu CC: gr...@nmr.mgh.harvard.edu Subject: 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. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
Re: [Freesurfer] caudate and putamen to surface
The caudate and putamen are not on the cortical surface. I'm confused as to what you are trying to do. On 04/10/2014 08:52 AM, gong jinnan wrote: Dear all, I want to use caudate and putamen as seed in surface to do PROBTRACK in FSL. For doing that, I acquired target surface which in the cortex seed using kris_convert and label2surf script. But I met some problems in extracting caudate and putamen in the surface. At first I used mdi_extract_label sub1/mri/aseg.auto.noCCseg.mgz 11 /test/L_Caudate.mgz” and it generated L_Caudate.mgz correctly. And then in order to do mri_vol2surf I did bbregister used “bbregister —s sub1 —mov sub1/mri/brain —init-fsl —reg sub1/mri/register.dat”. Then “mdi_vol2surf —src /test/L_Caudate.mgz —srcreg sub1/mri/register.dat —promfrac 0.5 —hemi lh —out /test/L_Caudate2surf.mgz”. Everything looked like went well by the time. But it’s weird when “mri_binarize —i /test/L_Caudate2surf.mgz —min 0.5 —o /test/L_Caudate2surf_bin.mgz” , it showed “Dound 0 values in range” and “Found 0 voxels in final mask”. I checked /test/L_Caudate.mgz and found it was correct. I am wondering is that because of register.dat which I am not very clear how to acquire it correctly? Or is that because lh.white was default used in mri_vol2surf? Could you give me any advises to work around this program? And may be about how to acquire register.dat in this context and how to transform this kind of ROI to surface. Thanks a lot! Sincerely, Jinnan ___ 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.
Re: [Freesurfer] mris_divide_parcellation same divisions between subjects
no, I was in subjects_dir. Updated the command to this and it works now.
thanks.
mri_aparc2aseg --s FGH_09112013 --labelwm --hypo-as-wm --rip-unknown
--volmask --o FGH_09112013/mri/wmdivided.mgz --annot aparc.split
On Thu, Apr 10, 2014 at 11:24 AM, Douglas N Greve gr...@nmr.mgh.harvard.edu
wrote:
Are you in the folder just above the mri folder?
On 04/10/2014 11:20 AM, Corinna Bauer wrote:
Hi Doug,
Following the example in recon-all.log, I tried this: mri_aparc2aseg
--s FGH_09112013 --labelwm --hypo-as-wm --rip-unknown --volmask --o
mri/wmdivided.mgz --annot aparc.split
and received and mgh Write error.mghWrite(mri/wmdivided.mgz, -1):
could not open file
On Thu, Apr 10, 2014 at 11:11 AM, Douglas N Greve
gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote:
Use mri_aparc2aseg with the --labelwm option. Look in the
recon-all.log
file for an example command line that generates wmparc.mgz
doug
On 04/10/2014 09:52 AM, Corinna Bauer wrote:
For creating corresponding wm segmentations to the rois derived
from
mris_divide_parcellation, should mri_aparc2wmseg be used or should
I
follow the steps outlined in this posting
https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2010-February/013471.html
?
Thanks
Corinna
On Wed, Apr 9, 2014 at 10:28 AM, Corinna Bauer
corinna...@gmail.com mailto:corinna...@gmail.com
mailto:corinna...@gmail.com mailto:corinna...@gmail.com
wrote:
Perfect. Thanks!
On Wed, Apr 9, 2014 at 10:22 AM, 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:
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
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 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
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 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)
[Freesurfer] Easy automated workflow for separating non-contiguous labels
Hi Freesurfers, Some of the Freesurfer annotations (specifically the Yeo atlases) have multiple disconnected regions with the same label. What's the best way to separate these annotations (or the labels produced by mri_annotation2label) so that I can get multiple label files where each label has all contiguous vertices? In other words, I want to do something like a clustering procedure, and I'd like to stay on the surface. Can this be done (easily)? Thanks Michael ___ 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] select_talairach_point function?
Hi I just find out how to launch the command, it is in the terminal where tksurfer is running, after the % sign. (I didn't understand what the tcl window was meaning) Best Celine 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 ___ 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] Post-doctoral Research Position at Columbia University
Post-doctoral Research Position at Columbia University A postdoctoral research position is currently available at Columbia University and the New York State Psychiatric Institute. Candidates must have completed a PhD in clinical, developmental, or cognitive neuroscience, or a related field. Research focuses on translational and developmental neuroimaging. Candidate should be interested in multimodal MRI techniques, attentional and related disorders in children and young adults, and the development of biomarkers of treatment response. Candidates with experience in the following areas are preferred: a) Computer programming skills (e.g., in C/C++, Python, MATLAB) b) Facility in operating of one or more common neuroimaging packages (e.g., AFNI, FSL, or SPM) Applicants should email their CV to Jonathan Posner, MD: jep2...@columbia.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Large areas of white matter ignored, even with control points
Hi Andrea, Take a look at the ?h.orig.nofix surfaces. Does it look like the wm edits were picked up in those initial surfaces? Also, just check that the edits to the wm.mgz were 255 and that there are no major disconnects anywhere. -Louis On Fri, 4 Apr 2014, Andrea Grant wrote: I was able to quickly edit my WM.mgz file using the contour edit that Louis suggested. However, when I then re-run the recon-all with -autorecon2-wm and -autorecon3, it doesn't correct the problem. I'm attaching two figures (with and without the edited WM.mgz overlay). What are my next steps to correct the segmentation? Thanks, Andrea On Fri, Mar 7, 2014 at 3:25 PM, Louis Nicholas Vinke vi...@nmr.mgh.harvard.edu wrote: Hi Andrea, You can use the contour tool in the voxel edit mode to quickly and roughly fill in wm. Use the tool with the wm.mgz selected in the volume layer list but set the brainmask (or T1) as the reference. Set brush value to 255, and then do crtl+alt+leftbutton while dragging the mouse to adjust the contour, and then crtl+leftclick to fill in selected regions. Note that the cerebellar white matter may be outlined by the contour as well, but if it doesn't connect with the cortical wm then it won't be filled in. -Louis ___ 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] Vertexwise surface area value?
Hi all, I am trying to extract vertexwise surface area values in an ascii files. For that I am doing mri_surf2surf --hemi ?h --srcsubject subject dir area --src_type curv --trgsubject fsaverage --trgsurfval XYZ-area --trg_type curv mris_convert -c XYZ-area ?h.white XYZ-area.asc However I am getting surface area values for some vertices as negative. 1) Am I following correct steps while writing vertex-wise values in ascii files? 2) Aren't values of surface-area supposed to be non-negative? I am not sure what I am missing here. Thanks for the help. -Sabin___ 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] longitudinal template generation with manual registration
Hi Andreas, It is extremely different to get good registrations manually (as you have to work in 3D and you only see 2D planes), and you'll most certainly not be able to achieve the accuracy of an automated method (especially not of robust_register/robust_template, which are pretty damn accurate, if you ask me :-). So I strongly advise against that (unless you want to show that manual registration messes things up). Now to answer your question: You could theoretically use mri_robust_template to construct the template from your three inputs. Then stop the stream, mri_concatenate_lta your transform from image_i to image_0 with the transform that roubst_template gives you from image_0 to template. Then reconstruct the template using mri_robust_template with --ixform (passing these transforms) and --noit to not iterate, this will recreate the median template image. Also replace the lta files in the base/mri/transforms with the new ones that you got from the concatenation, so that the base and later the long streams know. Resume the recon-all stream. This, obviously, has never been tested and requires some looking into recon-all to make sure you do things right. E.g. you need to use the norm.mgz of the inputs and make sure you overwrite the norm_template or similar (the one that get's created in the base step). Best, Martin On 04/09/2014 05:35 AM, Andreas Werner wrote: 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 -- Martin Reuter, Ph.D. Instructor in Neurology Harvard Medical School Assistant in Neuroscience Dept. of Radiology, Massachusetts General Hospital Dept. of Neurology, Massachusetts General Hospital Research Affiliate Computer Science and Artificial Intelligence Lab, Dept. of Electrical Engineering and Computer Science, Massachusetts Institute of Technology A.A.Martinos Center for Biomedical Imaging 149 Thirteenth Street, Suite 2301 Charlestown, MA 02129 Phone: +1-617-724-5652 Email: mreu...@nmr.mgh.harvard.edu reu...@mit.edu Web : http://reuter.mit.edu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] caudate and putamen to surface
Hi Prof. Greve, Thanks for your reply. Sorry, perhaps I have made some mistake in my data analysis. I just want to show tractography results of basal ganglia in surface space using FSL. Could transform fit_paths.nii.gz to surface be a brief way? In order to do mdi_vol2surf (transform volume ROIs in T1 space to surface) I should have register.dat. Is that a correct way to get it using bbregister --s SubID --mov T1.nii --init-fsl --reg register.dat Sincerely, Jinnan ___ 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
Thanks for pointing this binary out- I didn't realize the user could access it outside of recon-all. I've had a look at the fswiki for mris_sphere and it doesn't seem to be complete. I used it in the following format but not sure if this is correct: mris_sphere -n 160 -w 20 -scale 1 lh.orig lh.sphere_test I want to check that the above command converts lh.org to a sphere in 160 iterations, writes out every 20th iteration and ensures the area is preserved? Also, on the fswiki site: mris_sphere [options] surface file patch file name output patch I'm not certain if output patch is synonymous with output surface? Also, what is the purpose of a patch file name? Thanks. Date: Thu, 10 Apr 2014 11:30:15 -0400 From: fis...@nmr.mgh.harvard.edu To: xuelongz...@hotmail.com CC: freesurfer@nmr.mgh.harvard.edu; gr...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Intermediate stages of cortical inflation yes, many of our binaries take the -w n flag to write out a snapshot of the minimization every nth step, including mris_sphere cheers Bruce On Thu, 10 Apr 2014, Xuelong Zhao wrote: Is it also possible to track the inflation all the way to the sphere? I was hoping that I could take snapshots of equi-area intermediate forms as the cortex is unfolded onto the sphere instead of stopping at the inflated cortex. Thanks. Date: Wed, 9 Apr 2014 08:31:46 -0400 From: fis...@nmr.mgh.harvard.edu To: freesurfer@nmr.mgh.harvard.edu CC: gr...@nmr.mgh.harvard.edu Subject: 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. ___ 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.
