[Freesurfer] FW: Functional group analysis
Dear FreeSurfer team, I'm working on a functional analysis using FreeSurfer. I've already preprocessed my fMRI data and now I would like to analyze this data using mri_glmfit. My input is the prepared beta estimates for the fmri data (regression coefficients) and two groups (with activated regions for different muscles in the hand; musculus abductor digiti minimi vs first dorsal interossei). I do not want to smooth my data. Which command/step do you suggest in order to implement this data into mri_glm? I've experimented with mris_preproc and the creation of a FSGD-file in the structural analysis in order to implement my data in the GLM. Best, Silas From: silasniel...@hotmail.com To: freesurfer@nmr.mgh.harvard.edu Subject: Functional group analysis Date: Fri, 19 Jun 2015 14:26:20 +0200 Dear FreeSurfer team, I'm currently doing a functional group analysis using FreeSurfer by following your tutorial: https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastTutorialV5.1/FsFastGroupLevel - in order to concatenate the subjects data into one file you suggest using the command isxconcat-sess. My questions is; is it possible to use the command mris_preproc as in the structural analysis in this step? I simply want to project functional beta-values onto the fsaverage surface and analyze if there is a statistical significant difference between two groups (after correcting for multiple comparisons). Best, Silas ___ 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] recon-all pipeline for (sub-millimeter) 7T data
Hello! I wrote a bash script some time ago to process data acquired at a sub-millimeter resolution following the nice wiki entry of Falk Lüsebrink (https://surfer.nmr.mgh.harvard.edu/fswiki/HiResRecon). I thought it might be helpful for others, too, as there are some questions about it in the mailing list archives, so here it is: https://github.com/thomastweets/freesurfer-7t-pipeline. I am happy about any comments! Best, Thomas ___ 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] Fwd: Recon-all different execution time for same subjects
Dear freesurfer experts, I'm performing a study about the variability of the execution time of recon-all. I noticed that the execution of recon-all in Freesurfer 5.3 for two identical MRIs (two copies of the same MRI), takes different execution time. I'm performing the execution using GPUs capability, but the same is happening for the CPU-only executions. Checking the output logs I found i.e CA Reg, the number of the iterations is different, what's the main source of this variability? I guess that maybe It is related to some random seeds used and the convergence of the implemented methods. CA Reg example: Execution Time 1 - Subject 1: 00:25:23 Execution Time 2 - Subject 1: 00:32:14 In both cases the computing node was used exclusively for the recon-all execution. Did you measured the percentage of this variability? Can we extract some measures to compare the work realized in each execution? I'm thinking on the number of GPU kernels executed, the number of the iterations of the methods... Thank you in advance, -- Jordi Delgado Mengual PIC (Port d'Informació Científica) http://www.pic.es Avis - Aviso - Legal Notice: http://www.ifae.es/legal.html ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only for the person to whom it is addressed. If you believe this e-mail was sent to you in error and the e-mail contains patient information, please contact the Partners Compliance HelpLine at http://www.partners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail.
Re: [Freesurfer] Freesurfer tool for children's data
Hi Kristina what age? It works reasonably well down to 7 or even 5. Younger than that is something that Lilla Zollei has made a lot of progress on, but isn't ready for distribution yet cheers Bruce On Wed, 24 Jun 2015, Mayer Kristina wrote: Dear all, I was wondering if your free surfer pipeline (recon-all) is now available for children's data. If so, is there a page where it is described? Best wishes, Kristina ___ 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] Freesurfer tool for children's data
Dear all, I was wondering if your free surfer pipeline (recon-all) is now available for children's data. If so, is there a page where it is described? Best wishes, Kristina ___ 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] FS Developer v6 Hippocampal Segmentation
Hello, We’re going to be rerunning FS Recon-all using the newest version of FS v6 developer’s edition. Before any data is pre-processed, we wanted to receive input from other users on their own experience using it, specifically the Hippocampal subfield segmentation protocol. Are people receiving any unusual errors? Is there a lower resolution or less accurate segmentation of other cortical or subcortical structures? Any input would be great. Cheers, Noah Markowitz ___ 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] cortical parcelling with freesurfer
Hi Martin and Bruce,
Thanks for your replies!
I thought, maybe I am wrong, that a reference subject could be the best choice
for my purposes.
however, in principle, can I do the same procedure as you described for my
reference subject as well?
or similarly, can I use MNI standard surface, creating the annot file I desire
and going for mri_surf2surf to get the mapping on each subject?
Best wishes
Antonio
Hi Antonio,
why not draw your labels on fsaverage, and then map them to each subject (look
at mri_surf2surf or mri_label2label, mri_segstats ). In my opinion you don't
need the do all the registration of volumes, you only work on surfaces.
Probably someone here can give you the exact commands for creating an
annotation, mapping it to the subjects and computing stats.
Best, Martin
Hi Antonio
if you want the parcels to be in register you should use the sphere.reg instead
of the sphere file in mris_make_face_parcellation.
I'll leave the other questions for Doug:)
Bruce
Da: Napolitano Antonio
Inviato: martedì 23 giugno 2015 16.13
A: freesurfer@nmr.mgh.harvard.edu
Oggetto: cortical parcelling with freesurfer
Dear freesurfer experts,
I am having few questions about using freesurfer to finely (1000) parcel
cortical structures consistently through subjects.
Since I cannot do GCs atlas on my own, the main idea is running recon_all for
all of them and then register via mri_cvs_register all subjects to one; first
question: shall I run bbregister before mri_cvs_register or the latter will
take care of everything?
Once I have done that I do parcel the cortical stuff in the reference subject
by using the command:
mris_make_face_parcellation ${SUBJECTS_DIR}/${subjid}/surf/lh.sphere
${FREESURFER_HOME}/lib/bem/ic3.tri ${SUBJECTS_DIR}/${subjid}/label/lh.ic3.annot
I am not sure if that is correct...any hints will be very appreciated.
After that I am facing the problem of translating the lh.ic3.annot to the
surface of each subject in his original space; running mri_cvs_register I get
two resampled pial (lh.resample.pial and lh.dbg_surf.pial: I am not sure which
one must be used and I am not sure what is the difference between them), but
how can I get the parcellation back to the space of each suject? Mri_vol2vol
seems to be working with volumes only whereas I would need to apply the m3z to
surfaces. Shall I convert the annot to label and then to volumes so that I can
apply the warping directly to the volumes or is there a shortcut way to do so?
I am little bit stack at the moment and I would really thankful for any help or
suggestions.
Best Wishes
Antonio
Il tuo 5 per mille al Progetto ospedale senza dolore
Lavoriamo per il controllo del dolore nei bambini
e la diminuzione dell'ansia e dello stress nei genitori.
Ci aiuti anche tu?
Dona il tuo 5 X Mille
all'Ospedale Pediatrico Bambino Gesù
CF 80403930581 (sezione Ricerca Sanitaria)?
___
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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
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[Freesurfer] FW: reg-feat2anat update
Hi FS experts, Sorry for re-posting, but I never heard back and would love to get this working! Any ideas on why my download didn't work or if there is a new location of the new reg-feat2anat version? Thank you! Gabriella From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Hirsch, Gabriella Sent: Monday, June 22, 2015 4:53 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] reg-feat2anat update Hi FS experts, I had a quick query I was hoping you could help with; I am trying to load functional data analyzed in FSL in Freesurfer using reg-feat2anat (http://freesurfer.net/fswiki/FsTutorial/RegisterFeatOntoAnatomical) and seem to be having the same problem as the person in this thread: https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2014-June/038639.htmlhttps://mail.nmr.mgh.harvard.edu/pipermail/freesurfer/2014-June/038639.html In other words, the anat2exf.register.dat file is not being created. I tried to download the new version of reg-feat2anat posted by Doug in the thread but I'm getting an error when downloading with wget: no such file reg-feat2anat Has the location of this file changed? Thank you! Best, Gabriella ___ 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] cortical parcelling with freesurfer
I wouldn't do it in MNI coords - that won't be accurate in cortex. A
reference subject (fsaverage) would be fine
cheers
Bruce
On Wed, 24 Jun 2015, Napolitano
Antonio wrote:
Hi Martin and Bruce,
Thanks for your replies!
I thought, maybe I am wrong, that a reference subject could be the best choi
ce for my purposes.
however, in principle, can I do the same procedure as you described for my r
eference subject as well?
or similarly, can I use MNI standard surface, creating the annot file I desi
re and going for mri_surf2surf to get the mapping on each subject?
Best wishes
Antonio
Hi Antonio,
why not draw your labels on fsaverage, and then map them to each subject
(look at mri_surf2surf or mri_label2label, mri_segstats ). In my opinion you
don't need the do all the registration of volumes, you only work on
surfaces. Probably someone here can give you the exact commands for creating
an annotation, mapping it to the subjects and computing stats.
Best, Martin
Hi Antonio
if you want the parcels to be in register you should use the sphere.reg
instead of the sphere file in mris_make_face_parcellation.
I'll leave the other questions for Doug:)
Bruce
Da: Napolitano Antonio
Inviato: martedì 23 giugno 2015 16.13
A: freesurfer@nmr.mgh.harvard.edu
Oggetto: cortical parcelling with freesurfer
Dear freesurfer experts,
I am having few questions about using freesurfer to finely (1000) parcel
cortical structures consistently through subjects.
Since I cannot do GCs atlas on my own, the main idea is running recon_all
for all of them and then register via mri_cvs_register all subjects to one;
first question: shall I run bbregister before mri_cvs_register or the latter
will take care of everything?
Once I have done that I do parcel the cortical stuff in the reference
subject by using the command:
mris_make_face_parcellation ${SUBJECTS_DIR}/${subjid}/surf/lh.sphere
${FREESURFER_HOME}/lib/bem/ic3.tri
${SUBJECTS_DIR}/${subjid}/label/lh.ic3.annot
I am not sure if that is correct...any hints will be very appreciated.
After that I am facing the problem of translating the lh.ic3.annot to the
surface of each subject in his original space; running mri_cvs_register I
get two resampled pial (lh.resample.pial and lh.dbg_surf.pial: I am not sure
which one must be used and I am not sure what is the difference between
them), but how can I get the parcellation back to the space of each suject?
Mri_vol2vol seems to be working with volumes only whereas I would need to
apply the m3z to surfaces. Shall I convert the annot to label and then to
volumes so that I can apply the warping directly to the volumes or is there
a shortcut way to do so?
I am little bit stack at the moment and I would really thankful for any help
or suggestions.
Best Wishes
Antonio
Il tuo 5 per mille al Progetto ospedale senza dolore
Lavoriamo per il controllo del dolore nei bambini
e la diminuzione dell’ansia e dello stress nei genitori.
Ci aiuti anche tu?
Dona il tuo 5 X Mille
all’Ospedale Pediatrico Bambino Gesù
CF 80403930581 (sezione Ricerca Sanitaria)
___
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] FS Developer v6 Hippocampal Segmentation
Hi Noah, I cannot provide you with an unbiased opinion of the new subfield module, but something you can do is to download the development version and run the subfield code on data processed with FS 5.3 (assuming you have some), in order to get an idea of what the segmentations look like. Cheers, Eugenio Juan Eugenio Iglesias Postdoctoral researcher BCBL www.jeiglesias.com www.bcbl.eu Legal disclaimer/Aviso legal/Lege-oharra: www.bcbl.eu/legal-disclaimer - Original Message - From: Noah Markowitz noahb.markow...@gmail.com To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, June 25, 2015 5:03:28 AM Subject: [Freesurfer] FS Developer v6 Hippocampal Segmentation Hello, We’re going to be rerunning FS Recon-all using the newest version of FS v6 developer’s edition. Before any data is pre-processed, we wanted to receive input from other users on their own experience using it, specifically the Hippocampal subfield segmentation protocol. Are people receiving any unusual errors? Is there a lower resolution or less accurate segmentation of other cortical or subcortical structures? Any input would be great. Cheers, Noah Markowitz ___ 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
