[Freesurfer] CentOS 5.8

Dear FreeSurferers Just a quick question. Is CentOS 5.8 fully compatible with FS 5.3? Thank you. Kim ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this

[Freesurfer] tkmedit.bin: Command not found

Hello, I have just installed freesurfer in my linux ubuntu12.04 machine. I am getting error such as : *tkmedit.bin: Command not found* but the recon-all --help is working perfectly. My environment variable is working. Please help me where i m going wrong asap. Saurabh T.

Re: [Freesurfer] tkmedit.bin: Command not found

Hi Saurabh can you run: ls $FREESURFER_HOME/tktools/tkmedit.bin and see if it finds it? cheers Bruce On Mon, 3 Feb 2014, Saurabh Thakur wrote: Hello, I have just installed freesurfer in my linux ubuntu12.04 machine. I am getting error such as : tkmedit.bin: Command not found but the

Re: [Freesurfer] tkmedit.bin: Command not found

Hi Bruce, Thanks for such quick reply. please help me But when i m running..i m getting error as *bash: /usr/local/freesurfer/tktools/tkmedia.bin : No such file or directory.* but when i m running recon-all --help it is giving me all the options and information. I am not getting why

[Freesurfer] calculating spc on lobes annotation in longitudinal structural analysis

Dear all, I'm trying to get thickness spc stats for the individual lobe labels (specifically the frontal lobe) I created per subject per time point (in subject's longitudinal analysis template space) using: mri_annotation2label --subject $i --hemi ?h --lobesStrict ?h.lobes I've run

[Freesurfer] Difficulties with including hypo-intense areas (MS-lesions) as white matter without additionally transforming the lesion into normal white matter.

Hi, I would like to include unregistered hypo-intense lesions into white matter (as now they are excluded from cortex, and not registered as anything) without transforming the lesion from hypo-intense to normal (110). Is it possible to include these areas in white matter and additionally keep the

Re: [Freesurfer] Destrieux Atlas with Kid brains

Hi Mher, Just a bit of clarification in addition to last week's correspondence. If you are only looking at using the Destrieux atlas and not necessarily the whole FS recon pipeline you might be OK, as the folds don't change much in the age range of your interest. I woudl still monitor the

Re: [Freesurfer] Difficulties with including hypo-intense areas (MS-lesions) as white matter without additionally transforming the lesion into normal white matter.

Hi Linn I'm not sure I understand, but if you can paste them into the aseg.mgz as hypointensities I think things should work properly cheers Bruce On Mon, 3 Feb 2014, Linn Christin Bonaventure Norbom wrote: Hi,   I would like to include unregistered hypo-intense lesions into white matter

Re: [Freesurfer] CentOS 5.8

Kim, Yes, the CentOS4 build of freesurfer is compatible with CentOS5. You can download it from this page: http://surfer.nmr.mgh.harvard.edu/fswiki/Download -Zeke On 02/03/2014 04:45 AM, jh kim wrote: Dear FreeSurferers Just a quick question. Is CentOS 5.8 fully compatible with FS 5.3?

Re: [Freesurfer] Fwd: Difficulties with including hypo-intense areas (MS-lesions) as white matter without additionally transforming the lesion into normal white matter.

use mri_binarize --replace 77 2 --i aseg.mgz --o aseg.linn.mgz use the mri_binarize from here ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_binarize then use something like this to generate the new stats table (you'll have to customize it) mri_segstats --seg

Re: [Freesurfer] Fwd: Difficulties with including hypo-intense areas (MS-lesions) as white matter without additionally transforming the lesion into normal white matter.

Hi Linn it looks like a hypo intense region surrounded by a hyper-intense one, no? I think if you edit those voxels in the aseg.mgz to be white matter hypointensities or lesion then run the recon from there forward it should be ok Bruce On Mon, 3 Feb 2014, Linn Christin Bonaventure Norbom

Re: [Freesurfer] mri_convert error during make_average_subject

Bruce, I tried again on a set of different subjects, it error'd out once again. I have write permission, this is the same directory I've been using for quite some time, and I am positive there is space on the drive. These are the last 50 or so lines of the output before it stops:

[Freesurfer] Hippocampal subfields script.

Hi Eugenio: I have HSF data on 60 Asperger brains. Is there a script that will allow me to extract the volumes into a single location? thanks so much, Alan Francis Martinos Center ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Hippocampal subfields script.

Thanks Eugenio. On Mon, Feb 3, 2014 at 2:57 PM, Juan Eugenio Iglesias igles...@nmr.mgh.harvard.edu wrote: Hi Alan, there's indeed such a script: kvlQuantifyHippocampalSubfieldSegmentations.sh Check out the documentation at:

Re: [Freesurfer] Create a surf from a special volume?

Hi again, It is certainly a beginners question, and probably the code examples given below are not right... Is there anyone that could advice me how to do this? Thanks so much! Markus 2014-02-01 Markus Gschwind markus.gschw...@gmail.com: Dear all, I want to create a surface of a partially

Re: [Freesurfer] mris_divide_parcellation replication

Hi Christian and Martin mris_divide_parcellation finds the primary eigen-axis of the parcellation along the cortical surface, then splits it up into as many units as specified (either enough to get it under the area threshold, or explicitly specifed in a split file) cheers Bruce p.s. the

Re: [Freesurfer] mri_convert error during make_average_subject

Hi Jon can you include your entire command line so we can see it? thanks Bruce On Mon, 3 Feb 2014, Jonathan Holt wrote: Bruce, I tried again on a set of different subjects, it error'd out once again. I have write permission, this is the same directory I've been using for quite some time,

Re: [Freesurfer] Create a surf from a special volume?

Hi Markus the --s option should be a subject name, not a path to a volume cheers Bruce On Mon, 3 Feb 2014, Markus Gschwind wrote: Hi again, It is certainly a beginners question, and probably the code examples given below are not right... Is there anyone that could advice me how to do this?

Re: [Freesurfer] mri_convert error during make_average_subject

All, [1]+ Exit 1 nohup make_average_subject --subjects s_090803sk.long.SKtemplate/ s_091202sk.long.SKtemplate/ test.log On Mon, Feb 3, 2014 at 3:28 PM, Bruce Fischl fis...@nmr.mgh.harvard.eduwrote: Hi Jon can you include your entire command line so we can see it? thanks Bruce On

Re: [Freesurfer] mri_convert error during make_average_subject

and can you send us the output? On Mon, 3 Feb 2014, Jonathan Holt wrote: All, [1]+  Exit 1 nohup make_average_subject --subjects s_090803sk.long.SKtemplate/ s_091202sk.long.SKtemplate/ test.log On Mon, Feb 3, 2014 at 3:28 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Jon

[Freesurfer] Difference between aseg.stats and mri_segstats

Hi All, I'm interested in the cerebellar volume on a particular subject and I was wondering why I am seeing a slight difference between the volume listed in aseg.stats and the volume produced by mri_segstats with aseg.mgz as the input. It's a very slight difference, 44452mm^3 vs 45137.7mm^3

Re: [Freesurfer] Create a surf from a special volume?

Hi Bruce, Thank you! The creation of register.data worked perfectly. Now in order to create the mesh file (I suppose .w) of the altered brain with cut out temporal lobe (brain_T1fin), would this command be OK? mri_vol2surf --src FREESURFER/mri/brain_T1fin.nii.gz --srcreg

Re: [Freesurfer] Difference between aseg.stats and mri_segstats

aseg.stats is computed with partial volume correction. doug On 02/03/2014 04:07 PM, Jonathan Holt wrote: Hi All, I'm interested in the cerebellar volume on a particular subject and I was wondering why I am seeing a slight difference between the volume listed in aseg.stats and the volume

Re: [Freesurfer] Create a surf from a special volume?

mri_vol2surf will produce an overlay, not a surface. If you want an overlay, use .nii or .mgh instead of .w or .gii (no need for --out_type) doug On 02/03/2014 04:33 PM, Markus Gschwind wrote: Hi Bruce, Thank you! The creation of register.data worked perfectly. Now in order to create the

Re: [Freesurfer] Create a surf from a special volume?

Please remember to post to the list. Thanks! You cannot do that with mri_vol2surf. You'll have to create a binarization of the white matter, then use mrs_tessellate doug On 02/03/2014 05:24 PM, Markus Gschwind wrote: Thank you Doug! But actually I want to produce a *surface*, not an

Re: [Freesurfer] mri_convert error during make_average_subject

Remove the forward slash at the end of each subject name doug On 02/03/2014 04:04 PM, Jonathan Holt wrote: Here you are, attached! On Mon, Feb 3, 2014 at 3:54 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu mailto:fis...@nmr.mgh.harvard.edu wrote: and can you send us the output? On

Re: [Freesurfer] Freesurfer, Matlab and Maverick

Dear Sebastian, Im still working on my problem. I tried to put a symbolic link to the matlab binary and got the following answer: bash-3.2$ ln -s /Users/dhirjak/MATLAB_R2013a.app/bin/matlab /Users/dhirjak/bin/matlab ln: /Users/dhirjak/bin/matlab: No such file or directory bash-3.2$ ln -s

Re: [Freesurfer] Freesurfer, Matlab and Maverick

permission denied means that you don't have write permission into /Users/dhirjak/freesurfer/matlab/matlab you have to set up a link to a folder that is in your path On 02/03/2014 05:42 PM, Dusan Hirjak wrote: Dear Sebastian, Im still working on my problem. I tried to put a symbolic link to

Re: [Freesurfer] CentOS 5.8

Dear Zeke Thanks for the advice Kim 2014-02-04 Z K zkauf...@nmr.mgh.harvard.edu: Kim, Yes, the CentOS4 build of freesurfer is compatible with CentOS5. You can download it from this page: http://surfer.nmr.mgh.harvard.edu/fswiki/Download -Zeke On 02/03/2014 04:45 AM, jh kim wrote:

[Freesurfer] Mean diffusivity

Dear freesurfer experts, Can u please advise on how to extract the mean diffusivity value for each ROI from the wmparc file ? I know how to extract the FA value, but interested in the MD value also for the same regions. Thanks Rotem Rotem Saar-Ashkenazy Department of Brain and Cognitive Science

[Freesurfer] tkmedit is not working

Hi Everyone, Terminal output is: ///--// saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$* tkmedit* /usr/local/freesurfer/tktools*/tkmedit.bin: Command not found.*

[Freesurfer] FreeSurfer build stamps do not match

Hello Everyone, I am getting error /===/// saurabh@saurabh-Dell-System-XPS-L502X:/usr/local/freesurfer$ recon-all -s bert -all -hippo-subfields WARNING: tcsh v6.17.06 has an exit code bug! Please update tcsh! INFO*: FreeSurfer build stamps

[Freesurfer] Installation error

Hello everyone, Can u anyone help me in simplest and best way to install freesurfer on *i m not able to run command : * *1. tkmedit 2. tksurfer.System specification: * Dell laptop Ubuntu 12.04 LTS RAM 8Gb Graphics cards: Nvidia cards 1 Gb Thanks in advance. Saurabh Thakur,