Re: [Freesurfer] hippocampal subfields
Hi again,
The software requires approximately 10GB of RAM
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: Erik O'Hanlon erikohan...@rcsi.ie
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Tue, 26 May 2015 12:16:00 +0200 (CEST)
Subject: Re: [Freesurfer] hippocampal subfields
html
head
style!-- .EmailQuote { margin-left: 1pt; padding-left: 4pt; border-left:
#80 2px solid; } --/style
/head
body
font size=2span style=font-size:10pt;
div class=PlainTextHi Eugenio,br
br
I#39;m trying to run in on a cluster and I think I have eight cores assigned
with 2GB per core. I#39;m not sure if the process is parallelised though so it
could be the case that I have the job running on one of the possible core and
only using 2GB of RAM. I can
ask the cluster support team to check but is it possible to run the job across
the 8 cores and thus grab the 16GB of RAM or will the code only use the
onenbsp; core and I will have to get the RAM assigned to it to be
increased.br
br
Any guidance much appreciated and maybe if you could outline a typical system
requirement/setup to run a job. I have 200 subjects so your advice would
super.br
br
Thanks againbr
br
Cheersbr
br
Erikbr
br
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias
[e.igles...@bcbl.eu]br
Sent: 26 May 2015 10:33br
To: Freesurfer support listbr
Subject: Re: [Freesurfer] hippocampal subfieldsbr
br
Hi Erik,br
I guess your process was killed by the kernel. Maybe you ran out of RAM memory?
How much RAM do you have?br
Cheers,br
/Eugeniobr
br
Juan Eugenio Iglesiasbr
Postdoctoral researcher BCBLbr
a href=http://www.jeiglesias.com; target=_blankwww.jeiglesias.com/abr
a href=http://www.bcbl.eu; target=_blankwww.bcbl.eu/abr
br
Legal disclaimer/Aviso legal/Lege-oharra: a
href=http://www.bcbl.eu/legal-disclaimer; target=_blank
www.bcbl.eu/legal-disclaimer/abr
br
br
- Original Message -br
From: quot;Erik O#39;Hanlonquot; lt;erikohan...@rcsi.iegt;br
To: quot;Freesurfer support listquot;
lt;freesurfer@nmr.mgh.harvard.edugt;br
Sent: Monday, May 25, 2015 6:53:54 PMbr
Subject: Re: [Freesurfer] hippocampal subfieldsbr
br
br
br
Hi FS Experts,br
br
I#39;m trying the v6 hippocampal subfield code on a subject processed with
5.3.0 and I encountered the following error in the log filebr
br
Making Unknown map to reduced label 13br
Computing hyperparameters for estimation of Gaussian parametersbr
Estimating typical intensities of alveusbr
/home/support/tcin/apps/freesurfer/6-dev/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh:
line 43: 2675 Killed
quot;${exe_dir}quot;/segmentSubjectT1_autoEstimateAlveusML $argsbr
~br
br
It appears that the process finished prematurely and didn#39;t write out
anything in the mri/ dir.br
br
Any pointers how to resolve ? Any help greatly appreciatedbr
br
Cheersbr
br
Erikbr
br
Erik O#39;Hanlonbr
Postdoctoral researcherbr
br
br
br
br
RCSI Psychiatrybr
Royal College of Surgeons in Irelandbr
Beaumont Road, Beaumont, D9, Irelandbr
T: 8093740br
E: erikohan...@rcsi.ie W: a href=http://www.rcsi.ie;
target=_blankwww.rcsi.ie/abr
br
RCSI DEVELOPING HEALTHCARE LEADERSbr
WHO MAKE A DIFFERENCE WORLDWIDEbr
br
From: Erik O#39;Hanlonbr
Sent: 08 May 2015 19:10br
To: Freesurfer support listbr
Subject: RE: [Freesurfer] hippocampal subfieldsbr
br
That is super Nick,br
br
I#39;ll download it next week and try it out. Will I need to just run the
subfield part based on the 5.3.0 analysis I have or do it from scratch with the
beta v6?br
br
Thanks again for all the helpbr
br
Erikbr
br
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Nick Schmansky, MGH
[ni...@nmr.mgh.harvard.edu]br
Sent: 08 May 2015 19:05br
To: Freesurfer support listbr
Subject: Re: [Freesurfer] hippocampal subfieldsbr
br
Erik,br
br
If you wanted to test a #39;beta#39; of v6, which has the new hippocampalbr
stream, then our current internal #39;dev#39; build, which is very close
tobr
being the upcoming v6, can be downloaded from here:br
br
a href=ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/;
target=_blankftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev//abr
br
This goes for anyone else on the list who would like to help us test v6br
prior to release.br
br
Nickbr
br
br
On Fri, 2015-05-08 at 13:36 +, Erik O#39;Hanlon wrote:br
gt; Hi Eugenio,br
gt;br
gt; That#39;s brilliant, thanks so much for the quick response. So I willbr
gt; download the v6 code and how do I call the command so that it runs thebr
gt; v6 subfield analysis from the recon_all command?br
gt;br
gt; Thanks again for the guidance. Very much appreciatedbr
gt;br
gt; Cheersbr
gt;br
gt; Erikbr
gt;
[Freesurfer] Dev Version
Hi I downloaded the centos 6 freeview.bin and replaced it into $freesurferhome/bin/freeview.bin but now i cant open freeview, it says that it is not a executable file and it is binary. i wanted to test hippocampal subfields. Kind regards ___ 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] Hippocamp subfields
Hi Angela, It will work with subjects processed with the previous version; however, I would recommend (if possible) to run everything with the same version, for the sake of reproducibility. 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: angela favaro angela.fav...@unipd.it To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu Sent: Monday, May 25, 2015 1:55:17 PM Subject: Re: [Freesurfer] Hippocamp subfields THank you Zeke! Do I have to repeat all the reconall command with the new freesurfer version or I can use the processed files and run only the hippo segmentation? BW Angela You can download the dev version of freesurfer which contains the new hippocampal segmentation from the following page: https://surfer.nmr.mgh.harvard.edu/fswiki/Download -Zeke On May 23, 2015, at 11:07 AM, angela.fav...@unipd.it wrote: Hi Bruce, I would like to test the beta version of the new hippocampal subfields segmentation function. Is it at all possible to get it and how? BW Angela yes, but the ones in V6 (which someday will make it out) are more accurate. You can get a beta and try them out if you want. cheers Bruce On Fri, 22 May 2015, Hassan bakhshi wrote: Hi, I am using freesurfer v5.3, can I have hippocamp subfields in this version?? Kind regards ___ 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 ___ 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] hippocampal subfields
Hi Erik,
I guess your process was killed by the kernel. Maybe you ran out of RAM memory?
How much RAM do you have?
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: Erik O'Hanlon erikohan...@rcsi.ie
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Monday, May 25, 2015 6:53:54 PM
Subject: Re: [Freesurfer] hippocampal subfields
Hi FS Experts,
I'm trying the v6 hippocampal subfield code on a subject processed with 5.3.0
and I encountered the following error in the log file
Making Unknown map to reduced label 13
Computing hyperparameters for estimation of Gaussian parameters
Estimating typical intensities of alveus
/home/support/tcin/apps/freesurfer/6-dev/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh:
line 43: 2675 Killed ${exe_dir}/segmentSubjectT1_autoEstimateAlveusML $args
~
It appears that the process finished prematurely and didn't write out anything
in the mri/ dir.
Any pointers how to resolve ? Any help greatly appreciated
Cheers
Erik
Erik O'Hanlon
Postdoctoral researcher
RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont, D9, Ireland
T: 8093740
E: erikohan...@rcsi.ie W: www.rcsi.ie
RCSI DEVELOPING HEALTHCARE LEADERS
WHO MAKE A DIFFERENCE WORLDWIDE
From: Erik O'Hanlon
Sent: 08 May 2015 19:10
To: Freesurfer support list
Subject: RE: [Freesurfer] hippocampal subfields
That is super Nick,
I'll download it next week and try it out. Will I need to just run the subfield
part based on the 5.3.0 analysis I have or do it from scratch with the beta v6?
Thanks again for all the help
Erik
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Nick Schmansky, MGH
[ni...@nmr.mgh.harvard.edu]
Sent: 08 May 2015 19:05
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfields
Erik,
If you wanted to test a 'beta' of v6, which has the new hippocampal
stream, then our current internal 'dev' build, which is very close to
being the upcoming v6, can be downloaded from here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/
This goes for anyone else on the list who would like to help us test v6
prior to release.
Nick
On Fri, 2015-05-08 at 13:36 +, Erik O'Hanlon wrote:
Hi Eugenio,
That's brilliant, thanks so much for the quick response. So I will
download the v6 code and how do I call the command so that it runs the
v6 subfield analysis from the recon_all command?
Thanks again for the guidance. Very much appreciated
Cheers
Erik
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias
[e.igles...@bcbl.eu]
Sent: 08 May 2015 13:16
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfields
Hi Erik,
the 6.0 subfield code won't overwrite your 5.3 results, so if you run
the 6.0 module on data analyzed with 5.3, both results will co-exist
in the MRI directory of each subject.
Kind regards,
/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: Erik O'Hanlon erikohan...@rcsi.ie
To: freesurfer@nmr.mgh.harvard.edu
Sent: Friday, May 8, 2015 2:07:18 PM
Subject: [Freesurfer] hippocampal subfields
Hi FS experts,
I completed an analysis including the hippocampal subfield options
using 5.3.0. I understand that the subfield options was then removed
and I noticed that the new rev of the subfield code will be ready for
the v6 FS update. Can I use this code with my 5.3.0 code and if so
what files /dirs will I have to remove and how can I run or rerun it
to get the new subfield measures if it's possible. I would really like
to obtain the subfield measures and am not sure if I can use the
existing measures based on the 5.3.0 code. Any advice would be very
much appreciated.
Kind regards and thanks in advance
Erik
Erik O'Hanlon
Postdoctoral researcher
RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont, D9, Ireland
T: 8093740
E: erikohan...@rcsi.ie W: www.rcsi.ie
RCSI DEVELOPING HEALTHCARE LEADERS
WHO MAKE A DIFFERENCE WORLDWIDE
___
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
[Freesurfer] Recon-all Error
Hello, I had the problem which was the recon-all error at Fix Topology lh stage for 6 of 12 subjects i ran freesurfer. Bruce then told me to check the lh.orig.nofix and lh.inflated.nofix to see if there is part of skull or cerebellum. But when i want to open them with this command: tkmedit lh.orig.nofix it says that it cant open file . How can i check these files to see where is the problem for these 6 subjects. Kind Regards ___ 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] hippocampal subfields
Hi Eugenio,
I'm trying to run in on a cluster and I think I have eight cores assigned with 2GB per core. I'm not sure if the process is parallelised though so it could be the case that I have the job running on one of the possible core and only using 2GB of RAM. I can
ask the cluster support team to check but is it possible to run the job across the 8 cores and thus grab the 16GB of RAM or will the code only use the one core and I will have to get the RAM assigned to it to be increased.
Any guidance much appreciated and maybe if you could outline a typical system requirement/setup to run a job. I have 200 subjects so your advice would super.
Thanks again
Cheers
Erik
From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias [e.igles...@bcbl.eu]
Sent: 26 May 2015 10:33
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfields
Hi Erik,
I guess your process was killed by the kernel. Maybe you ran out of RAM memory? How much RAM do you have?
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: Erik O'Hanlon erikohan...@rcsi.ie
To: Freesurfer support list freesurfer@nmr.mgh.harvard.edu
Sent: Monday, May 25, 2015 6:53:54 PM
Subject: Re: [Freesurfer] hippocampal subfields
Hi FS Experts,
I'm trying the v6 hippocampal subfield code on a subject processed with 5.3.0 and I encountered the following error in the log file
Making Unknown map to reduced label 13
Computing hyperparameters for estimation of Gaussian parameters
Estimating typical intensities of alveus
/home/support/tcin/apps/freesurfer/6-dev/bin/run_segmentSubjectT1_autoEstimateAlveusML.sh: line 43: 2675 Killed ${exe_dir}/segmentSubjectT1_autoEstimateAlveusML $args
~
It appears that the process finished prematurely and didn't write out anything in the mri/ dir.
Any pointers how to resolve ? Any help greatly appreciated
Cheers
Erik
Erik O'Hanlon
Postdoctoral researcher
RCSI Psychiatry
Royal College of Surgeons in Ireland
Beaumont Road, Beaumont, D9, Ireland
T: 8093740
E: erikohan...@rcsi.ie W: www.rcsi.ie
RCSI DEVELOPING HEALTHCARE LEADERS
WHO MAKE A DIFFERENCE WORLDWIDE
From: Erik O'Hanlon
Sent: 08 May 2015 19:10
To: Freesurfer support list
Subject: RE: [Freesurfer] hippocampal subfields
That is super Nick,
I'll download it next week and try it out. Will I need to just run the subfield part based on the 5.3.0 analysis I have or do it from scratch with the beta v6?
Thanks again for all the help
Erik
From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Nick Schmansky, MGH [ni...@nmr.mgh.harvard.edu]
Sent: 08 May 2015 19:05
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfields
Erik,
If you wanted to test a 'beta' of v6, which has the new hippocampal
stream, then our current internal 'dev' build, which is very close to
being the upcoming v6, can be downloaded from here:
ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/dev/
This goes for anyone else on the list who would like to help us test v6
prior to release.
Nick
On Fri, 2015-05-08 at 13:36 , Erik O'Hanlon wrote:
Hi Eugenio,
That's brilliant, thanks so much for the quick response. So I will
download the v6 code and how do I call the command so that it runs the
v6 subfield analysis from the recon_all command?
Thanks again for the guidance. Very much appreciated
Cheers
Erik
From: freesurfer-boun...@nmr.mgh.harvard.edu
[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Eugenio Iglesias
[e.igles...@bcbl.eu]
Sent: 08 May 2015 13:16
To: Freesurfer support list
Subject: Re: [Freesurfer] hippocampal subfields
Hi Erik,
the 6.0 subfield code won't overwrite your 5.3 results, so if you run
the 6.0 module on data analyzed with 5.3, both results will co-exist
in the MRI directory of each subject.
Kind regards,
/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: Erik O'Hanlon erikohan...@rcsi.ie
To: freesurfer@nmr.mgh.harvard.edu
Sent: Friday, May 8, 2015 2:07:18 PM
Subject: [Freesurfer] hippocampal subfields
Hi FS experts,
I completed an analysis including the hippocampal subfield options
using 5.3.0. I understand that the subfield options was then removed
and I noticed that the new rev of the subfield code will be ready for
the v6 FS update. Can I use this code with my 5.3.0 code and if so
what files /dirs will I have to remove and how can I run or rerun it
to get the new subfield measures if it's possible. I would really
[Freesurfer] Diffrence Between stat files and mris
Hi, I wanted to ask what is the difference between stat files result and the mris_anatomical_stats? can we get the same result using both? i want to get the anatomical thickness of temporal gyruses such as superior temporal gyrus thickness, and non neocortex volumes like hippocamp and amygdala volume! Kind regards ___ 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] Dev Version
Did you check the permissions? You have to make sure the permissions are executable. HTH D On 5/26/15 6:33 AM, Hassan bakhshi wrote: Hi I downloaded the centos 6 freeview.bin and replaced it into $freesurferhome/bin/freeview.bin but now i cant open freeview, it says that it is not a executable file and it is binary. i wanted to test hippocampal subfields. Kind regards ___ 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] Recon-all Error
Hi Hassan that's not the correct command line for tkmedit. You are probably better off using freeview in any case though, once you make the binary executable. cheers Bruce On Tue, 26 May 2015, Hassan bakhshi wrote: Hello, I had the problem which was the recon-all error at Fix Topology lh stage for 6 of 12 subjects i ran freesurfer. Bruce then told me to check the lh.orig.nofix and lh.inflated.nofix to see if there is part of skull or cerebellum. But when i want to open them with this command: tkmedit lh.orig.nofix it says that it cant open file . How can i check these files to see where is the problem for these 6 subjects. Kind Regards ___ 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_label2annot: surf/rh.orig No such file or directory
no ./rh.unknown.label was created. Yawu On Mon, May 25, 2015 at 7:22 PM, Douglas Greve gr...@nmr.mgh.harvard.edu wrote: Is there a file called ./rh.unknown.label ? On 5/25/15 5:37 AM, Liu Y wrote: Dear Freesurfers, I tried to generate annotations by using the command mris_label2annot --s K_TS66 --h rh --ctab aparc.annot.ctab --a Liu --nhits nhits.mgh. But Could not succeed. Any helps would be appreciated. --- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/Liu/freesurfer FSFAST_HOME /home/Liu/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /home/Liu/freesurfer/subjects MNI_DIR /home/Liu/freesurfer/mni FSL_DIR /usr/local/fsl under folder /home/Liu/freesurfer/subjects/K_TS66/label, I run mris_label2annot --s K_TS66 --h rh --ctab aparc.annot.ctab --a Liu --nhits nhits.mgh. output: Reading ctab aparc.annot.ctab Number of ctab entries 36 INFO: no labels specified, generating from ctab 0 ./rh.unknown.label 1 ./rh.bankssts.label 2 ./rh.caudalanteriorcingulate.label 3 ./rh.caudalmiddlefrontal.label 4 ./rh.corpuscallosum.label 5 ./rh.cuneus.label 6 ./rh.entorhinal.label 7 ./rh.fusiform.label 8 ./rh.inferiorparietal.label 9 ./rh.inferiortemporal.label 10 ./rh.isthmuscingulate.label 11 ./rh.lateraloccipital.label 12 ./rh.lateralorbitofrontal.label 13 ./rh.lingual.label 14 ./rh.medialorbitofrontal.label 15 ./rh.middletemporal.label 16 ./rh.parahippocampal.label 17 ./rh.paracentral.label 18 ./rh.parsopercularis.label 19 ./rh.parsorbitalis.label 20 ./rh.parstriangularis.label 21 ./rh.pericalcarine.label 22 ./rh.postcentral.label 23 ./rh.posteriorcingulate.label 24 ./rh.precentral.label 25 ./rh.precuneus.label 26 ./rh.rostralanteriorcingulate.label 27 ./rh.rostralmiddlefrontal.label 28 ./rh.superiorfrontal.label 29 ./rh.superiorparietal.label 30 ./rh.superiortemporal.label 31 ./rh.supramarginal.label 32 ./rh.frontalpole.label 33 ./rh.temporalpole.label 34 ./rh.transversetemporal.label 35 ./rh.insula.label $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /home/Liu/freesurfer/subjects/K_TS66/label cmdline mris_label2annot --s K_TS66 --h rh --ctab aparc.annot.ctab --a Liu --nhits nhits.mgh sysname Linux hostname D4201Z machine x86_64 user Liu subject K_TS66 hemirh SUBJECTS_DIR /home/Liu/freesurfer/subjects ColorTable aparc.annot.ctab AnnotName Liu NHitsFile nhits.mgh nlables 36 LabelThresh 0 0.00 Loading /home/Liu/freesurfer/subjects/K_TS66/surf/rh.orig No such file or directory mris_label2annot: could not open label file ./rh.unknown.label No such file or directory ERROR: reading ./rh.unknown.label There is indeed a rh.orig file under /home/Liu/freesurfer/subjects/K_TS66/surf/ Thanks, Yawu ___ Freesurfer mailing listfreesur...@nmr.mgh.harvard.eduhttps://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 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] average subject
Hi Sofia can you email us the command line you ran to create the average subject and its output? thanks Bruce On Tue, 26 May 2015, Sofia Rodriguez Penuela wrote: Dear Freesurfers, after running the average subject with Freesurfer 5.3, the files T1.mgz and Orig.mgz were not created in the fsaverage folder. Where could be the proble m? Thank you in advance. Best regards, Sofia ___ 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] Diffrence Between stat files and mris
Hi Hassan the cortical stats are generated by mris_anatomical_stats while the noncortical ones (like hippocampal volume) by mri_segstats. The results of each are tabulated in each subject's stats dir. cheers Bruce On Tue, 26 May 2015, Hassan bakhshi wrote: Hi, I wanted to ask what is the difference between stat files result and the mris_anatomical_stats? can we get the same result using both? i want to get the anatomical thickness of temporal gyruses such as superior temporal gyrus thickness, and non neocortex volumes like hippocamp and amygdala volume! Kind regards ___ 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] Dev Version
Hi Hassan try: chmod a+x FREESURFER_HOME/bin/freeview.bin cheers Bruce On Tue, 26 May 2015, Hassan bakhshi wrote: Hi I downloaded the centos 6 freeview.bin and replaced it into $freesurferhome/bin/freeview.bin but now i cant open freeview, it says that it is not a executable file and it is binary. i wanted to test hippocampal subfields. Kind regards ___ 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] FW: correcting for brain size
Thanks David! Gabriella From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of David Vazquez Sent: Friday, May 22, 2015 6:19 PM To: Freesurfer support list Subject: Re: [Freesurfer] FW: correcting for brain size Hi Gabriella, I'm not an expert in freesurfer. I've worked with freesurfer for 5 years now. When we started I had the same problem when including ICV in the qdec table and running it as a nuisance variable. I'm assuming you have ICV in mm^3. Try converting it to cm^3 or dcm^3 in your qdec table. That worked for us. I think qdec might have a problem with numbers in the millions/hundred thousands. Just don't forget to reconvert when you are interpreting/writing your results or else it can get confusing. Maybe its just us, but when we use ICV as a covariate many, many significant clusters were diminished to nothing. Hope this helps. -David Vazquez PhD candidate in Cognitive Neuroscience University of California, Riverside NSF GRFP fellow On Fri, May 22, 2015 at 6:16 AM Hirsch, Gabriella gabriella_hir...@meei.harvard.edumailto:gabriella_hir...@meei.harvard.edu wrote: HI FS experts, I haven’t heard back and am still wrestling with these questions. Any takers? I’d really appreciate any thoughts at all if possible. Thanks, Gabriella From: Hirsch, Gabriella Sent: Wednesday, May 20, 2015 3:55 PM To: freesurfer@nmr.mgh.harvard.edumailto:freesurfer@nmr.mgh.harvard.edu Subject: ICV correction for volume analysis Hi FreeSurfer experts, I have a couple quick questions I’m hoping someone can clarify for me; I am conducting a group surface-based morphometry analysis in all three measures in 2 groups (patient and control) and am looking for the best way to correct for brain size variability in the cortical volume analysis. My question is: 1. So far, I’ve been using Qdec, however qdec seems to crash when I ask it to pose ICV as a nuisance factor. In the archives, we are told to “mean center” the ICV values in order for Qdec to take it, but I was informed that mean centering was not a good idea in morphometry studies. Any thoughts? 2. I’ve found that in QDEC, if I include ICV AND global mean volume as nuisance factors, the analysis works. If I only include ONE of the two variables, it crashes. This is super frustrating – is there any way around this issue? 3. If I want to keep only the raw ICV values in my analysis (i.e. not demean it), what’s the best way to go about this? Do I have to re-run the analysis using mri_glmfit with the ICV values as a covariate in my fsgd file (with a contrast like 1 -1 0 0, with age and ICV as covariates)? I tried doing it this way and got some questionable results. I want to make sure I’m executing this correctly. I’d really appreciate any help on this. Thank you! Gabriella ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edumailto: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] error mni152 reg
Hello Freesurfer mni152reg --s 0201JB-anat = mkdir: cannot create directory `/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.31253': Permission denied. Thus I put this command following the way of searching freesurfer mail support. chmod ugo+w /usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.31253 chmod: cannot access `/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.31253': No such file or directory I am using freesurver 5.3 and FDL 5. 0.7. Please let me know what should I do. Thank you. Linux gencess 2.6.32-504.1.3.el6.x86_64 #1 SMP Tue Nov 11 17:57:25 UTC 2014 x86_64 x86_64 x86_64 GNU/Linux fslregister --mov /usr/pubsw/packages/fsl/current/data/standard/MNI152_T1_2mm_brain.nii.gz --s 0201JB-anat --reg /autofs/cluster/catanagp/users/jumi/subjects/AD/0201JB/0201JB-anat/mri/transforms/reg.mni152.2mm.dat --dof 12 mkdir: cannot create directory `/usr/pubsw/packages/fsl/current/data/standard/tmp.fslregister.31253': Permission denied ___ 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] Stats file question
Hello Freesurfer team, When generating the .stats files for grey matter volumetric data, this information appears in multiple places and I'm not sure which data I should be using for my final results. There appears to be cortical information generated in both the .stats file based off the DKT atlas and the l/rh.aparc.stats file. The information in these files is quite different from one another. Using the FreeSurferColorLUT.txt (as listed in the recon-all dev table) instead of WMParcStatsLUT.txt (which is used when running recon-all) in generating the mri_segstats wmparc.stats file also produces cortical volumetric data. This third set of data differs significantly from the DKT Atlas, and differs less-so from the cortical volumes produced in the aparc.stats file. Which of the .stats files containing grey matter volume data is most accurate? Best, Kody J. Zalewski ___ 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] error in atlas creation
Hi Anthony sorry, I know you've posted this before. What version are you running? And what type is your labeled data? That is, are they uchar? int? At some point this used to not work with non-uchar data, but I think I fixed it a while ago. YOu might try downloading a beta of V6 and see if it fixes your problem cheers Bruce On Tue, 26 May 2015, Anthony Dick wrote: Hello, I have been stumped by this error I keep getting using the rebuild_gca_atlas.csh script. I am trying to build a cerebellar atlas, so I am wondering if the problem is with the brains we parcellated, or with my installation etc. The brains consist of manually segmented cerebellums from the original T1. The T1 is run through Freesurfer, and the ROIs are made in Freeview. The edited file is called seg_edited.mgz. Things run smoothly up until this error: using MR volume /path/subjects/4/mri/brain.mgz to mask input volume... reading 23 input volumes... logging results to talairach_one.log reading 'subjects/average/RB_one_2015-05-14.gca'... gcaAllocMax: node dims 32 32 32 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 average std = 8.4 using min determinant for regularization = 7.1 0 singular and 119 ill-conditioned covariance matrices regularized reading '/path/subjects/4/mri/nu.mgz'... reading '/path/subjects/average/RB_one_2015-05-14.gca'... gcaAllocMax: node dims 32 32 32 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading frame -1 of gca MRIcopyFrame: src and dst must be same type reading '/path/subjects/4/mri/transforms/talairach_one.lta'... mri_read(): couldn't determine type of file /path/subjects/4/mri/transforms/talairach_one.lta mri_em_register: could not open input volume /path/subjects/4/mri/transforms/talairach_one.lta. ___ 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] switch to freesurfer
Hi all, I'm used to getting cortical thickness/surface area/volume values using CIVET and minc-tools and I am trying to learn/convert to freesurfer tools. I want to perform a MACACC analysis. Can anyone recommend some good documentation about making the switch to freesurfer or which specific tools I should be looking at? Thank you very much! Melissa ___ 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] Problens with kvlEMSegment
Hello freesurfers, I am once again trying to run ex-vivos brains on freesurfer, with a new set of data. I am using freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 on a Intel® Core™ i7-2630QM CPU @ 2.00GHz × 8 running ubuntu 14.10 64-bit I was following the ex vivo suggested protocol ( http://freesurfer.net/fswiki/ExvivoRecon), however, when I try to start the white mater segmentation with kvlEMSegment, despite of any parameters I try to imput, I am getting this error: (...) Starting EM: *** Error in `kvlEMSegment': munmap_chunk(): invalid pointer: 0x7f67af3cb010 *** Abort (core dumped) or a similar error with a slightly different pointer code (ex: 0x7fc78a64d010). I couldn't find a similar error on the mail archive, or google. Does anyone knows what this means, and/or how can I avoid it? thanks for your time, Fabio Dalpra ___ 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] WM ROIs: Using wmparc.mgz from cvs_avg35_inMNI152 atlas
Sorry, I thought my original post would be somehow linked to the second one. Here it is: Dear Freesurfer experts, I would like to segment a WM skeleton I derived using FSL's TBSS into ROIs based on white matter regions as derived in the wmparc.mgz file. I thought of using the fsaverage subject, but it does not have the wmparc.mgz file; thus I plan to use the CVS atlas (cvs_avg35_inMNI152). My plan is to extract each relevant ROI from wmparc.mgz, transform it into a binary file in MNI space, then use it to mask my WM skeleton using fslstats. I used this example command to extract the left WM postcentral ROI: mri_extract_label /Applications/freesurfer/subjects/cvs_avg35_inMNI152/mri/wmparc.mgz 3022 wm-lh-postcentral.mgz Now I need to transform the resulting file into a binary file with the same orientation and space as the MNI152_1mm standard brain ($FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz) before using it with fslstats. Could you please point to me the commands in order to achieve this? Thank you. Estephan J. Moana-Filho, DDS, MS, PhD Clinical Assistant Professor TMD and Orofacial Pain Division U of MN School of Dentistry ___ 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_label2annot: surf/rh.orig No such file or directory
The error is ERROR: reading ./rh.unknown.label meaning that it is expecting it as input. You need to create it or change the command to not expect it On 05/26/2015 08:32 AM, Liu Y wrote: no ./rh.unknown.label was created. Yawu On Mon, May 25, 2015 at 7:22 PM, Douglas Greve gr...@nmr.mgh.harvard.edu mailto:gr...@nmr.mgh.harvard.edu wrote: Is there a file called ./rh.unknown.label ? On 5/25/15 5:37 AM, Liu Y wrote: Dear Freesurfers, I tried to generate annotations by using the command mris_label2annot --s K_TS66 --h rh --ctab aparc.annot.ctab --a Liu --nhits nhits.mgh. But Could not succeed. Any helps would be appreciated. --- freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0 Setting up environment for FreeSurfer/FS-FAST (and FSL) FREESURFER_HOME /home/Liu/freesurfer FSFAST_HOME /home/Liu/freesurfer/fsfast FSF_OUTPUT_FORMAT nii.gz SUBJECTS_DIR /home/Liu/freesurfer/subjects MNI_DIR /home/Liu/freesurfer/mni FSL_DIR /usr/local/fsl under folder /home/Liu/freesurfer/subjects/K_TS66/label, I run mris_label2annot --s K_TS66 --h rh --ctab aparc.annot.ctab --a Liu --nhits nhits.mgh. output: Reading ctab aparc.annot.ctab Number of ctab entries 36 INFO: no labels specified, generating from ctab 0 ./rh.unknown.label 1 ./rh.bankssts.label 2 ./rh.caudalanteriorcingulate.label 3 ./rh.caudalmiddlefrontal.label 4 ./rh.corpuscallosum.label 5 ./rh.cuneus.label 6 ./rh.entorhinal.label 7 ./rh.fusiform.label 8 ./rh.inferiorparietal.label 9 ./rh.inferiortemporal.label 10 ./rh.isthmuscingulate.label 11 ./rh.lateraloccipital.label 12 ./rh.lateralorbitofrontal.label 13 ./rh.lingual.label 14 ./rh.medialorbitofrontal.label 15 ./rh.middletemporal.label 16 ./rh.parahippocampal.label 17 ./rh.paracentral.label 18 ./rh.parsopercularis.label 19 ./rh.parsorbitalis.label 20 ./rh.parstriangularis.label 21 ./rh.pericalcarine.label 22 ./rh.postcentral.label 23 ./rh.posteriorcingulate.label 24 ./rh.precentral.label 25 ./rh.precuneus.label 26 ./rh.rostralanteriorcingulate.label 27 ./rh.rostralmiddlefrontal.label 28 ./rh.superiorfrontal.label 29 ./rh.superiorparietal.label 30 ./rh.superiortemporal.label 31 ./rh.supramarginal.label 32 ./rh.frontalpole.label 33 ./rh.temporalpole.label 34 ./rh.transversetemporal.label 35 ./rh.insula.label $Id: mris_label2annot.c,v 1.17 2011/03/02 00:04:32 nicks Exp $ cwd /home/Liu/freesurfer/subjects/K_TS66/label cmdline mris_label2annot --s K_TS66 --h rh --ctab aparc.annot.ctab --a Liu --nhits nhits.mgh sysname Linux hostname D4201Z machine x86_64 user Liu subject K_TS66 hemirh SUBJECTS_DIR /home/Liu/freesurfer/subjects ColorTable aparc.annot.ctab AnnotName Liu NHitsFile nhits.mgh nlables 36 LabelThresh 0 0.00 Loading /home/Liu/freesurfer/subjects/K_TS66/surf/rh.orig No such file or directory mris_label2annot: could not open label file ./rh.unknown.label No such file or directory ERROR: reading ./rh.unknown.label There is indeed a rh.orig file under /home/Liu/freesurfer/subjects/K_TS66/surf/ Thanks, Yawu ___ 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 -- 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
[Freesurfer] error in atlas creation
Hello, I have been stumped by this error I keep getting using the rebuild_gca_atlas.csh script. I am trying to build a cerebellar atlas, so I am wondering if the problem is with the brains we parcellated, or with my installation etc. The brains consist of manually segmented cerebellums from the original T1. The T1 is run through Freesurfer, and the ROIs are made in Freeview. The edited file is called seg_edited.mgz. Things run smoothly up until this error: using MR volume /path/subjects/4/mri/brain.mgz to mask input volume... reading 23 input volumes... logging results to talairach_one.log reading 'subjects/average/RB_one_2015-05-14.gca'... gcaAllocMax: node dims 32 32 32 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 average std = 8.4 using min determinant for regularization = 7.1 0 singular and 119 ill-conditioned covariance matrices regularized reading '/path/subjects/4/mri/nu.mgz'... reading '/path/subjects/average/RB_one_2015-05-14.gca'... gcaAllocMax: node dims 32 32 32 gcaAllocMax: prior dims 128 128 128 gcaAllocMax: max_labels 0 reading frame -1 of gca MRIcopyFrame: src and dst must be same type reading '/path/subjects/4/mri/transforms/talairach_one.lta'... mri_read(): couldn't determine type of file /path/subjects/4/mri/transforms/talairach_one.lta mri_em_register: could not open input volume /path/subjects/4/mri/transforms/talairach_one.lta. -- Anthony Steven Dick, Ph.D. Assistant Professor Director, Cognitive Neuroscience Program and Graduate Certificate in Cognitive Neuroscience Department of Psychology Florida International University Modesto A. Maidique Campus AHC4 454 11200 S.W. 8th Street Miami, FL 33199 Ph: 305-348-4202; Lab Ph: 305-348-9055; Fx: 305-348-3879 Email: ad...@fiu.edu Webpage: faculty.fiu.edu/~adick; Lab Webpage: http://dcn.fiu.edu Join the Society for the Study of Human Development: http://www.sshdonline.org ___ 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] average subject
Please see surfer.nmr.mgh.harvard.edu/fswiki/BugReporting On 05/26/2015 03:24 AM, Sofia Rodriguez Penuela wrote: Dear Freesurfers, after running the average subject with Freesurfer 5.3, the files T1.mgz and Orig.mgz were not created in the fsaverage folder. Where could be the problem? Thank you in advance. Best regards, Sofia ___ 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] Diffrence Between stat files and mris
the surface-based stats file are produced by mris_anatomical_stats, the volume-based stats files are produced by mri_segstats. Not sure about your question doug On 05/26/2015 07:16 AM, Hassan bakhshi wrote: Hi, I wanted to ask what is the difference between stat files result and the mris_anatomical_stats? can we get the same result using both? i want to get the anatomical thickness of temporal gyruses such as superior temporal gyrus thickness, and non neocortex volumes like hippocamp and amygdala volume! Kind regards ___ 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] fs-fast primarily voxel based?
Some steps are volume-based and some are surface-based. Motion correction is voxel based. Slice-timing correction is done in the volume. It then gets sampled onto the surface where surface-based smoothing is done. The GLM analysis is done on the surface. I often use voxel and vertex interchangeably. doug On 05/25/2015 09:44 PM, lee.r...@csiro.au wrote: Hi all, I am seeking a little clarification regarding fMRI analyses with FS-FAST. In the documentation and supplied PowerPoint presentations there are many references to niftis, and statements like “Performs GLM fit at each voxel”. Given this, for the cortex, would I be correct in the assertion that fs-fast performs most steps using voxels, but smooths the data and displays the results using meshes? Many thanks, Lee ___ 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] Inquiry about error message when run 'Tracula'
Dear Anastasia, Thanks for your answer. I tried to replace 'bedpostx_mgh' with 'bedpostx' in the shell file 'tract-all' in order to run Tracula in the C2B2 server (Titan cluster). But it failed as well. Is there anyway to run Tracula, i.e., by pass the running error of bedpostx_mgh? Besides, I have two more questions when I set up a configuration file. 1) In the step9 of Tracula tutorial ( https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Tracula), i.e., Specify the b-value table, I can only set bvalfile to specify the location of the b-value table. Can I specify a different b value file for each of the scans in the study (with bvallist,for example) besides a single b value file for all scans in the study (with bvalfile). 2) About the number of low-b images. Since I will use 4D nifty images instead of raw DICOMs, I need to set the number of low-b images in the configuration file, i.e., set nb0. Can I specify a different nb0 value for each of the scans in the study (with nb0list,for example) besides a single nb0 value for all scans in the study. Best, Xiaofu On Fri, May 22, 2015 at 1:35 PM, Anastasia Yendiki ayend...@nmr.mgh.harvard.edu wrote: Hi Xiaofu - The bedpostx program is not configured to run on any type of cluster with any type of queueing software. It was originally written to be run on an SGE cluster with specific queue names. The bedpostx_mgh is a modified version that also works on our PBS cluster. Making it work on additional clusters would require additional tweaks, and it's impossible for us to make it work on everyone's cluster. In a future version, I'd like to give the option to simply print out all the necessary commands, and then it would be up to the user to figure out how to submit them as jobs on their own cluster. This is not implemented yet. a.y On Tue, 19 May 2015, Xiaofu wrote: Dear Sir/Madam, I tried to run Tracula in the C2B2 server at Columbia University. However, I got the following error message after submitted my job using qsub to the sever. I'd greatly appreciate it if you could help me resolve this problem. WARN: Running FSL's bedbost locally - this might take a while WARN: It is recommended to run this step on a cluster bedpostx_mgh -n 2 /DTIdata/Tracula/3789/dmri subjectdir is /DTIdata/Tracula/3789/dmri Making bedpostx directory structure Queuing preprocessing stages Unable to run job: Job was rejected because job requests unknown queue short.q. Exiting. Queuing parallel processing stage Unable to run job: Job was rejected because job requests unknown queue long.q. Exiting. Queuing post processing stage Unable to run job: Job was rejected because job requests unknown queue long.q. Exiting. Looking forward to hearing from you. Thank you very much. Best, Xiaofu ___ 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] switch to freesurfer
Hi Melissa, what is MACACC analysis? doug On 05/26/2015 12:42 PM, Melissa Levesque, Ms. wrote: Hi all, I'm used to getting cortical thickness/surface area/volume values using CIVET and minc-tools and I am trying to learn/convert to freesurfer tools. I want to perform a MACACC analysis. Can anyone recommend some good documentation about making the switch to freesurfer or which specific tools I should be looking at? Thank you very much! Melissa ___ 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] switch to freesurfer
Hi Melissa, please send responses to the list. Thanks! Yes, this is possible. You'll need to analyze each of your subjects in FreeSurfer with recon-all, QC them, then run mris_preproc, mri_surfsurf to smooth, then mri_glmfit and mri_glmfit-sim. See the tutorials that we have on our wiki. doug On 05/26/2015 01:06 PM, Melissa Levesque, Ms. wrote: It's an analysis to assess correlations in cortical thickness or surface area across the cortex or with a predictor variable. http://www.bic.mni.mcgill.ca/~jason/reprints/Lerch2006MACACC.pdf -- 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] WM ROIs: Using wmparc.mgz from cvs_avg35_inMNI152 atlas
what is the question? On 05/26/2015 12:55 PM, Estephan J. Moana-Filho wrote: Any suggestions? I've perused the freesurfer mailing list and couldn't find any advice specifically to this question. Estephan ___ 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] WM ROIs: Using wmparc.mgz from cvs_avg35_inMNI152 atlas
Any suggestions? I've perused the freesurfer mailing list and couldn't find any advice specifically to this question. Estephan ___ 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.
