Re: [Freesurfer] recon-all exited with ERRORS
External Email - Use Caution
If you are running Virtualbox to host linux on a windows machine sharing a
folder from a windows NTFS file system, then it may not work to create soft
links in linux on the mounted share w/o setting some things on the Windows
side. I’m not up on what current versions of VirtualBox support for
creating soft links in a linux file system on top of the (different) NTFS file
system, but here is some info from ~2 years
ago,https://secure-web.cisco.com/1FAdsc9WBYl3JetwHMp2nc_AR2rQlI8PlEU1VIVMmtW4AXXraRYQrh4EesIh-2zxLL95RZ4uADb94HhLf6bwC4HStrmNBxTN1P6onMGfuO2S4W4uvvwfGIBNqjQiVAZPmx6apNd4RkD__6429s9Dec_A80QMbmZ5p1jH5eSbN_Yy8sjxqJeDxkuw6X14AqP-wtxc7-bvAz65_QiVsYkX5NYR7HCd7X9LJ_qmhN6nk5ccXH_x6XDx5euZhGR99v6Dj/https%3A%2F%2Fstackoverflow.com%2Fquestions%2F56343002%2Fis-it-possible-to-use-symbolic-links-in-virtualbox-shared-folder-without-adminis
- R.
On Aug 5, 2021, at 10:20, Kiyotaka Nemoto kiyot...@nemotos.net
wrote:External Email - Use
CautionHi,I think the problem
is caused because Zhaoguanguses a VirtualBox share folder.The path
"/media/sf_T1/" indicates the path is a shared folder of VirtualBox.Symbolic
links can be used on some certain conditions.Source:MailScanner has
detected a possible fraud attempt from "secure-web.cisco.com" claiming to
behttps://secure-web.cisco.com/1SzkQ16diCzjzLRbWT9fZxbUN_qVihhNUAbkqhDWMHpIn3-M2UeXKZtomyLdGKz2hQxzBRgbN5ye_n05Zfy6i5YNSm-x-25yEjp6h819_yq-6XkkGYt7FEZuwuuolHCQWTR-sqNub0Pf4T8SZ5ech1a-XOt0R2j7pKbYcP2AiDn1AZEeiN-1FzCbzAd1OPrZdpQWmDKTLuEUcQI_l28duTwPlf-3v0aiOLOQGoQ_n2r2o86c1tP5E7kGLa3LF4bPG/https%3A%2F%2Fwww.virtualbox.org%2Fmanual%2FUserManual.html%23sharedfoldersI
think there are two workaround options..1. Avoid using shared folders
If you copy your T1 image from shared folder to somewhere on your Linux
guest, recon-all should go well.2. Change "ln -s" to "cp" in recon-all
I tweak recon-all a little bit so that recon-all works well with files
on VirtualBox shared folders. The commands below makes backup of
recon-all first, then substitute "ln -s" with "cp" or "cp -r"=cd
$FREESURFER_HOME/binsudo cp recon-all recon-all.origsudo sed -i 's/ln -s
\$hemi/cp \$hemi/' recon-allsudo sed -i 's/ln -s
\$FREESURFER_HOME\/subjects\/fsaverage/cp -r
\$FREESURFER_HOME\/subjects\/fsaverage \$SUBJECTS_DIR/' recon-allsudo sed -i
's/ln -s \$FREESURFER_HOME\/subjects\/\${hemi}.EC_average/cp -r
\$FREESURFER_HOME\/subjects\/\${hemi}.EC_average \$SUBJECTS_DIR/'
recon-all=Hope this helps,KiyotakaOn Thu, Aug 5, 2021 at 10:42 PM Douglas
N. Greve dgr...@mgh.harvard.edu wrote:Look in
/media/sf_T1/recon/demo3/surfDoes lh.white.preaparc.H exist?If so, does
lh.white.H exist?If not, what happens when you runln -s lh.white.preaparc.H
lh.white.Hin that folder?On 8/5/2021 1:41 AM, guang
wrote:External Email - Use
CautionHello FreeSurfer
Developers,I'm attempting to preprocess my nii.gz files with FreeSurfer, But
some errorsoccurred when I recon-all the data. I've attached
the batch script and recon-all.log in case it's of any use.1)
FreeSurfer version:
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0..0-2beb96c2) Platform: CentOS
release 6.10 (Final)3) uname -a: Linux bogon 2.6.32-754.2.1.el6.x86_64 #1 SMP
Fri Jul 13 12:50:12 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux4) recon-all.log:
see attached5) batch .shfile:seeattachedThank you for any
reply.zhaoguang___
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Re: [Freesurfer] Creating an Freesurfer .annot file from an MNI coordinate region of interest
Hi Paul Have you run recon-all on your data? If so, then there will be .annot files that you can use to look up what parcellation unit is at that coordinate in any given subject. Or closest to that coordinate as in general it may not be in the cortex Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Paul Dhami Sent: Thursday, August 5, 2021 5:00 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Creating an Freesurfer .annot file from an MNI coordinate region of interest External Email - Use Caution Dear FS community, My ultimate goal is to do a seed of interest connectivity analysis. Accordingly, I have MNI coordinates for a seed (e.g., left DLPFC). However, for the softwares I am using (CONN toolbox and Brainstorm), I need a .annot file which has the surface region of interest label I want to use as the seed. My problem is I do not know how to create an .annot file from MNI coordinates of my seed/region of interest. Can I create an .annot or label file with Freesurfer centered around an MNI coordinate, or would I first need to create a volume ROI using another software? Any directions as to how I can do this would be greatly appreciated. Best Wishes, Paul ___ 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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.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. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Re: [Freesurfer] recon-all exited with ERRORS
External Email - Use Caution
Hi,
I think the problem is caused because Zhaoguang uses a VirtualBox share
folder.
The path "/media/sf_T1/" indicates the path is a shared folder of
VirtualBox.
Symbolic links can be used on some certain conditions.
Source:
https://secure-web.cisco.com/1dwlgJDipuhkA56EdBKvdgjX7GQ06QB_tibWCFgxRVp5qMyNCdaPDbahbXesxHSWfDY3t8wvp6OTfje04KDpgHFGDdkoecJv07GtKeuldJJNVJnsuffSVx9LfYzLYeh-1a5ScJN1PdZ-fDNE--Lnv1R4phboTjurWMX43qna0wem5Wa2vhWvLXwEfcGTxqY7Bduq1xk_MKqmJ0BaQptL5lOK-V0kBUTl58fCB2eRrlvBQMoLDzBscjG_cnGqeT3ZMyhoh1X1rv5D7bkil9-4mWA/https%3A%2F%2Fwww.virtualbox.org%2Fmanual%2FUserManual.html%23sharedfolders
I think there are two workaround options.
1. Avoid using shared folders
If you copy your T1 image from shared folder to somewhere on your Linux
guest, recon-all should go well.
2. Change "ln -s" to "cp" in recon-all
I tweak recon-all a little bit so that recon-all works well with files
on VirtualBox shared folders.
The commands below makes backup of recon-all first, then substitute "ln
-s" with "cp" or "cp -r"
=
cd $FREESURFER_HOME/bin
sudo cp recon-all recon-all.orig
sudo sed -i 's/ln -s \$hemi/cp \$hemi/' recon-all
sudo sed -i 's/ln -s \$FREESURFER_HOME\/subjects\/fsaverage/cp -r
\$FREESURFER_HOME\/subjects\/fsaverage \$SUBJECTS_DIR/' recon-all
sudo sed -i 's/ln -s \$FREESURFER_HOME\/subjects\/\${hemi}.EC_average/cp -r
\$FREESURFER_HOME\/subjects\/\${hemi}.EC_average \$SUBJECTS_DIR/' recon-all
=
Hope this helps,
Kiyotaka
On Thu, Aug 5, 2021 at 10:42 PM Douglas N. Greve
wrote:
> Look in /media/sf_T1/recon/demo3/surf
> Does lh.white.preaparc.H exist?
> If so, does lh.white.H exist?
> If not, what happens when you run
> ln -s lh.white.preaparc.H lh.white.H
> in that folder?
>
>
>
> On 8/5/2021 1:41 AM, guang wrote:
>
> External Email - Use Caution
> Hello FreeSurfer Developers,
> I'm attempting to preprocess my nii.gz files with FreeSurfer, But some
> errors occurred when I recon-all the data. I've attached the batch script
> and recon-all.log in case it's of any use.
> 1) FreeSurfer version:
> freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
> 2) Platform: CentOS release 6.10 (Final)
> 3) uname -a: Linux bogon 2.6.32-754.2.1.el6.x86_64 #1 SMP Fri Jul 13
> 12:50:12 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux
> 4) recon-all.log: see attached
> 5) batch .sh file:see attached
>
> Thank you for any reply.
>
> zhaoguang
>
>
>
>
>
>
>
>
> ___
> Freesurfer mailing
> listfreesur...@nmr.mgh.harvard.eduhttps://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
>
>
> ___
> Freesurfer mailing list
> Freesurfer@nmr.mgh.harvard.edu
> https://secure-web.cisco.com/1-4gugTG7IJfnMSP9Kbd3NVtUKTt23hOeCLRtobg_9eugEF5QbPwyeJBMkyKRnUEycElhjwY_qKW8n3EOxMBUrO7rwxeCUSjp4j1qOzAxzrKpPV_RJTy1RSNxyqGUyCewq1f9iCpdF2RClubdfNt5C8jGFXfJPOAmLmiZk-4b-CGRZBCXllH9J5SMAGVEGteqtX-K_CxOOiuBZk0raFZN1xAeJl0qAqY_cFG8zTNfCs5wJBUhpuinkEL7eIZOHQhRGdZYRNiHtONcaVRD7crYlw/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer
> 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 Mass General
> Brigham Compliance HelpLine at
> http://secure-web.cisco.com/1MwgiO-I6rZmEaKP4aOBZdZ_lN3KTEvoI5tOu9SKhlrO_PjSav0ImSZjUWc6isdXJxz5MMet1p4a8vqcQSc8z7DNyPQ9UzO9tbZGawhyD4z2sdXaANthxnEH6C-Kd01XWSFmsfeNIgCkjPPrtHfQf2ldNJkcsc_68a560U4p8HW1kXnLcJK2-s-u9zKfCWu3nSu5n-OgnfnFfebyUOPY5fVUXpDRtbqxouQQv6phML8b3x6XMUqqMke9gyroDbRTWUdSbcH0NEosH9DEpE1Oj8Q/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline
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> sender of this message immediately. Continuing to send or respond to
> e-mail after receiving this message means you understand and accept this
> risk and wish to continue to communicate over unencrypted e-mail.
>
--
Kiyotaka Nemoto, M.D., Ph.D.
Associate Professor
Department of Psychiatry
Division of Clinical Medicine, Faculty of Medicine
University of Tsukuba
1-1-1 Tennodai Tsukuba, Ibaraki 305-8575, Japan
E-mail: kiyot...@nemotos.net
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Re: [Freesurfer] Creating an Freesurfer .annot file from an MNI coordinate region of interest
First, try running recon-all on the mni152 template Find the vertex closest to your seed coordinate You can create a circle on the surface with something like this (where vertexno is the vertex number you found above) mri_volsynth --dim nvertices 1 1 1 --pdf delta --delta-crsf vertexno 1 1 1 --o delta.mgz # create an overlay with all 0s except 1 at your target vertex mris_fwhm --so --niters 6 --i delta.mgz --o delta.sm6.mgz --s subject --hemi hemi # Smooth it out to a radius of ABOUT 6mm mri_binarize --i delta.sm6.mgz --min 0.01 --o roi.mgz # Binarize it This should give you a circle with a radius of about 6mm. You can play with the --niters to make it bigger or smaller. You can then use mri_cor2label to convert this to a label, eg, mri_cor2label --i roi.mgz --id 1 --o roi.label --surf mni152recon lh You can then convert the label to an annotation with mris_label2annot On 8/5/2021 4:59 AM, Paul Dhami wrote: External Email - Use Caution Dear FS community, My ultimate goal is to do a seed of interest connectivity analysis. Accordingly, I have MNI coordinates for a seed (e.g., left DLPFC). However, for the softwares I am using (CONN toolbox and Brainstorm), I need a .annot file which has the surface region of interest label I want to use as the seed. My problem is I do not know how to create an .annot file from MNI coordinates of my seed/region of interest. Can I create an .annot or label file with Freesurfer centered around an MNI coordinate, or would I first need to create a volume ROI using another software? Any directions as to how I can do this would be greatly appreciated. Best Wishes, Paul ___ 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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.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. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Re: [Freesurfer] recon-all exited with ERRORS
Look in /media/sf_T1/recon/demo3/surf Does lh.white.preaparc.H exist? If so, does lh.white.H exist? If not, what happens when you run ln -s lh.white.preaparc.H lh.white.H in that folder? On 8/5/2021 1:41 AM, guang wrote: External Email - Use Caution Hello FreeSurfer Developers, I'm attempting to preprocess my nii.gz files with FreeSurfer, But some errors occurred when I recon-all the data. I've attached the batch script and recon-all.log in case it's of any use. 1) FreeSurfer version: freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c 2) Platform: CentOS release 6.10 (Final) 3) uname -a: Linux bogon 2.6.32-754.2.1.el6.x86_64 #1 SMP Fri Jul 13 12:50:12 UTC 2018 x86_64 x86_64 x86_64 GNU/Linux 4) recon-all.log: see attached 5) batch .sh file:see attached Thank you for any reply. zhaoguang ___ 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 Mass General Brigham Compliance HelpLine at http://www.massgeneralbrigham.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. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail.
Re: [Freesurfer] How to join certain segmentation with T1.mgz and save them in one file with nifti format
what are the actual values ("black" does not mean much)
On 8/5/2021 1:21 AM, Ammar Shujaa wrote:
External Email - Use Caution
Hello FreeSurfur developers,
When I did:
mergeseg --src brainmask.bin.mgz --merge both.hippo.mgz --o bm+hippo.mgz
The color of the hippo segment (both.hippo) in the bm+hippo.mgz file
has become black. Is there any way I can do to change the color of
both.hippo segment from back to another color?
Thanks,
Ammar
On Thursday, August 5, 2021, 11:45:12 AM GMT+9, Douglas N. Greve
wrote:
To merge the two hippocampi together in one file you can
fscalc left-hippo.mgz sum right-hippo.mgz -o both.hippo.mgz
If you want a binary mask of the brainmask, you can run
mri_binarize --i brainmask.mgz --min 0.5 --o brainmask.bin.mgz
Then run
mergeseg --src brainmask.bin.mgz --merge both.hippo.mgz --o bm+hippo.mgz
On 8/4/2021 12:21 PM, Ammar Shujaa wrote:
External Email - Use Caution
Hello Freesufer developers,
I just want to know how to merge the right and left-hypocampus in one
file (hypocampus.gmz), and then merge hypocampus.gmz with
brainmask.gmz so that I can get one mgz file having the segmentations
with the brainmask. I want to use this file
(hypocampus+brainmask.gmz) in another software.
Best regards
Ammar
On Wednesday, August 4, 2021, 11:54:48 PM GMT+9, Douglas N. Greve
wrote:
I don't understand what you mean by "join". Can you elaborate?
On 8/4/2021 1:16 AM, Ammar Shujaa wrote:
External Email - Use Caution
Hello FreeSurfur Developers,
I have used binary mask and got the segmentations: right and
left-hypocampus.mgz.
I just want to know how to join these segmentations with T1.mgz so
that I can get one file containing T1 image with the two
segmentations. I also want to save the T1 image with the the
segmentions in nifti format.
Thanks in advance.
Ammar
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Re: [Freesurfer] How to join certain segmentation with T1.mgz and save them in one file with nifti format
External Email - Use Caution Hello FreeSurfur developers, When I did: mergeseg --src brainmask.bin.mgz --merge both.hippo.mgz --o bm+hippo.mgz The color of the hippo segment (both.hippo) in the bm+hippo.mgz file has become black. Is there any way I can do to change the color of both.hippo segment from back to another color? Thanks, Ammar On Thursday, August 5, 2021, 11:45:12 AM GMT+9, Douglas N. Greve wrote: To merge the two hippocampi together in one file you can fscalc left-hippo.mgz sum right-hippo.mgz -o both.hippo.mgz If you want a binary mask of the brainmask, you can run mri_binarize --i brainmask.mgz --min 0.5 --o brainmask.bin.mgz Then run mergeseg --src brainmask.bin.mgz --merge both.hippo.mgz --o bm+hippo.mgz On 8/4/2021 12:21 PM, Ammar Shujaa wrote: External Email - Use Caution Hello Freesufer developers, I just want to know how to merge the right and left-hypocampus in one file (hypocampus.gmz), and then merge hypocampus.gmz with brainmask.gmz so that I can get one mgz file having the segmentations with the brainmask. I want to use this file (hypocampus+brainmask.gmz) in another software. Best regards Ammar On Wednesday, August 4, 2021, 11:54:48 PM GMT+9, Douglas N. Greve wrote: I don't understand what you mean by "join". Can you elaborate? On 8/4/2021 1:16 AM, Ammar Shujaa wrote: External Email - Use Caution Hello FreeSurfur Developers, I have used binary mask and got the segmentations: right and left-hypocampus.mgz. I just want to know how to join these segmentations with T1.mgz so that I can get one file containing T1 image with the two segmentations. I also want to save the T1 image with the the segmentions in nifti format. Thanks in advance. Ammar ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1-3ndcvWjkjeTI9QKGnD85Gyh8wS1fHmP5stU-quLD4XSQ9TOishFP_dVjizlU4INbH0HabKUE8KVJkrqOAtdX0NpMmn7_4w7ySxdxmmC5yuL1NnpHnxUQRRSIiMsT_X0dQwVY1AqOMYj9UnV_ncAchpEO8GJZ81wnSvN2ubenPT8MzvFNimCzvjcGzGoFP6NnxT-vw4vpJ0fbKEjXv31ZOjZMXmlSKTI0w_xu7-OtJ7nFliDfYs1yhOPZq95iIjA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be https://secure-web.cisco.com/1-3ndcvWjkjeTI9QKGnD85Gyh8wS1fHmP5stU-quLD4XSQ9TOishFP_dVjizlU4INbH0HabKUE8KVJkrqOAtdX0NpMmn7_4w7ySxdxmmC5yuL1NnpHnxUQRRSIiMsT_X0dQwVY1AqOMYj9UnV_ncAchpEO8GJZ81wnSvN2ubenPT8MzvFNimCzvjcGzGoFP6NnxT-vw4vpJ0fbKEjXv31ZOjZMXmlSKTI0w_xu7-OtJ7nFliDfYs1yhOPZq95iIjA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer 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 Mass General Brigham Compliance HelpLine at MailScanner has detected a possible fraud attempt from "secure-web.cisco.com" claiming to be http://secure-web.cisco.com/1SkxMyDoMN2HT13DKDjDp-T3aOV6oKJZVJLTvu0hf4h79Tdd6ZgGbU0VPRmtp7u0ZelRG9oUTCGyNExKd1tVQSHV5S1oIHCPuneMYKn5tVKBE-k9kfpoT83YboosVqAmPq7diuRBYebQnJQOvMmTWM38reK6EO0DhAu_UeaSVWMT9JiwQpM5wX2OilQxlBSfEkqIV9QglJQfrEtjriSUEs0CD3KxAaiFQ-eaUNy5P16-TnnXTGJ1hf71ktO8ObqQ5/http%3A%2F%2Fwww.massgeneralbrigham.org%2Fcomplianceline . 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. Please note that this e-mail is not secure (encrypted). If you do not wish to continue communication over unencrypted e-mail, please notify the sender of this message immediately. Continuing to send or respond to e-mail after receiving this message means you understand and accept this risk and wish to continue to communicate over unencrypted e-mail. ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://secure-web.cisco.com/1-3ndcvWjkjeTI9QKGnD85Gyh8wS1fHmP5stU-quLD4XSQ9TOishFP_dVjizlU4INbH0HabKUE8KVJkrqOAtdX0NpMmn7_4w7ySxdxmmC5yuL1NnpHnxUQRRSIiMsT_X0dQwVY1AqOMYj9UnV_ncAchpEO8GJZ81wnSvN2ubenPT8MzvFNimCzvjcGzGoFP6NnxT-vw4vpJ0fbKEjXv31ZOjZMXmlSKTI0w_xu7-OtJ7nFliDfYs1yhOPZq95iIjA/https%3A%2F%2Fmail.nmr.mgh.harvard.edu%2Fmailman%2Flistinfo%2Ffreesurfer ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu
[Freesurfer] Creating an Freesurfer .annot file from an MNI coordinate region of interest
External Email - Use Caution Dear FS community, My ultimate goal is to do a seed of interest connectivity analysis. Accordingly, I have MNI coordinates for a seed (e.g., left DLPFC). However, for the softwares I am using (CONN toolbox and Brainstorm), I need a .annot file which has the surface region of interest label I want to use as the seed. My problem is I do not know how to create an .annot file from MNI coordinates of my seed/region of interest. Can I create an .annot or label file with Freesurfer centered around an MNI coordinate, or would I first need to create a volume ROI using another software? Any directions as to how I can do this would be greatly appreciated. Best Wishes, Paul ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer
