Re: [Freesurfer] mris_label2annot Error: FG1.mpm.vpnl not found in CTAB colortable_vpnl.txt

LBfs for data/bss: Layout problem > with segments 0 and 1: > > Segments would overlap. > > “ > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu < > freesurfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *LYU, TIANXIANG > *Sent:* Tuesday, May 7, 2024

Re: [Freesurfer] mris_label2annot Error: FG1.mpm.vpnl not found in CTAB colortable_vpnl.txt

...@nmr.mgh.harvard.edu On Behalf Of LYU, TIANXIANG Sent: Tuesday, May 7, 2024 8:36 AM To: Freesurfer support list Cc: 内田航 Subject: Re: [Freesurfer] mris_label2annot Error: FG1.mpm.vpnl not found in CTAB colortable_vpnl.txt External Email - Use Caution Dear Yujing, I hope this email finds you

Re: [Freesurfer] mris_label2annot Error: FG1.mpm.vpnl not found in CTAB colortable_vpnl.txt

rfer-boun...@nmr.mgh.harvard.edu> *On Behalf Of *LYU, TIANXIANG > *Sent:* Tuesday, May 7, 2024 12:30 AM > *To:* freesurfer@nmr.mgh.harvard.edu > *Cc:* 内田航 > *Subject:* [Freesurfer] mris_label2annot Error: FG1.mpm.vpnl not found in > CTAB colortable_vpnl.txt > > > > *

Re: [Freesurfer] mris_label2annot Error: FG1.mpm.vpnl not found in CTAB colortable_vpnl.txt

/average/colortable_BA_thresh.txt distribution/average/colortable_vpnl.txt 2. copy them to your average/ directory Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of LYU, TIANXIANG Sent: Tuesday, May 7, 2024 12:30 AM To: freesurfer@nmr.mgh.harvard.edu Cc: 内田航 Subject: [Freesurfer

Re: [Freesurfer] mris_label2annot

External Email - Use Caution Dear Yujing, Thank you so much for your answer. Everything works now. Best, Maria Czarnecka pt., 30 cze 2023 o 16:59 Maria Czarnecka napisał(a): > Dear Yujing, > > Thank you so much for your answer. > My ctab looks like this: > > 11100 Unknown

Re: [Freesurfer] mris_label2annot

, 2023 10:59 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mris_label2annot External Email - Use Caution Dear Yujing, Thank you so much for your answer. My ctab looks like this: 11100 Unknown 0 0 00 11102 G_and_S_occipital_inf

Re: [Freesurfer] mris_label2annot

External Email - Use Caution Dear Yujing, Thank you so much for your answer. My ctab looks like this: 11100 Unknown 0 0 00 11102 G_and_S_occipital_inf 0 0 00 1 G_cuneus 0 0 00 9 G_o

Re: [Freesurfer] mris_label2annot

, June 27, 2023 9:07 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] mris_label2annot External Email - Use Caution Dear Sisters and Brothers in neuroscience, I am trying to make my own annotation file that will include only occipital cortex labels from the a2009s atlas. Is it

[Freesurfer] mris_label2annot

External Email - Use Caution Dear Sisters and Brothers in neuroscience, I am trying to make my own annotation file that will include only occipital cortex labels from the a2009s atlas. Is it possible? I am trying to do that with: mris_label2annot --ctab lh.my-color-table.txt --a

Re: [Freesurfer] mris_label2annot seed not set

External Email - Use Caution Awesome, thank you for the information! Ben

Re: [Freesurfer] mris_label2annot seed not set

You can ignore that. That was put in by a contractor who put it into every source file that did not set the random see. No randomness is used in this program, so you are safe On 6/16/2022 9:58 AM, Benjamin Deck wrote: External Email - Use Caution Hi Freesurfer experts, While trying

[Freesurfer] mris_label2annot seed not set

External Email - Use Caution Hi Freesurfer experts, While trying to create a custom annotation file I get the following warning: mris_label2annot --s sub-DAEK --a yeo2011 --no-unknown --ctab sub-DAEK_yeoLUT.txt --ldir /mnt/c/Users/Ben/freesurfer/subjects/sub-DAEK/label/li2019_lab

Re: [Freesurfer] mris_label2annot - make all command exiting with errors

Sorry, there is not a good way in v7 On 4/7/2021 2:57 AM, Marion DURTESTE wrote: External Email - Use Caution Hi Douglas, Thank you very much for your answer! What would you suggest is therefore the best way to do this in V7? Best wishes, Marion D Le 2021-04-06 15:18, Douglas N. Gr

Re: [Freesurfer] mris_label2annot - make all command exiting with errors

External Email - Use Caution Hi Douglas, Thank you very much for your answer! What would you suggest is therefore the best way to do this in V7? Best wishes, Marion D Le 2021-04-06 15:18, Douglas N. Greve a écrit : > The "-make" functionality does not work in V7. We sh

Re: [Freesurfer] mris_label2annot - make all command exiting with errors

The "-make" functionality does not work in V7. We should have disabled that flag On 4/2/2021 3:41 AM, Marion DURTESTE wrote: External Email - Use Caution Dear FreeSurfer developers, When running*recon-all -make all *after correcting a few errors from the recon-all output, it exits w

[Freesurfer] mris_label2annot - make all command exiting with errors

External Email - Use Caution Dear FreeSurfer developers, When running RECON-ALL -MAKE ALL after correcting a few errors from the recon-all output, it exits with an error. This occurs when the mris_label2annot command is called. > Loading /Users/mariondurteste/Documents/PhD/Free

Re: [Freesurfer] mris_label2annot gives wrong label

External Email - Use Caution Sure. Thank you. mris_label2annot --s p6 --h rh --a t500 --ldir $SUBJECTS_DIR/p6/label/regenerated_rh_500 --nhits nhits.mgh --ctab /home/rachelsun/Software/freesurfer/resolution1015_LUT.txt Reading ctab /home/rachelsun/Software/freesurfer/resolution1

Re: [Freesurfer] mris_label2annot gives wrong label

can you send your command line and full terminal output? On 8/19/2019 9:24 PM, Rachel S wrote: External Email - Use Caution Hi Greve, Thank you for your prompt reply. I tried removing --l before. But it gave Mapping unhit to unknown Found 123407 unhit vertices None of the vertices wer

Re: [Freesurfer] mris_label2annot gives wrong label

External Email - Use Caution Hi Greve, Thank you for your prompt reply. I tried removing --l before. But it gave Mapping unhit to unknown Found 123407 unhit vertices None of the vertices were labeled. What could be the problem? Thank you. Best regards, Rachel Greve, Douglas

Re: [Freesurfer] mris_label2annot gives wrong label

You should remove the --l argument. That is incompatible with --ldir. On 8/19/19 5:50 PM, Rachel S wrote: > > External Email - Use Caution > > Hi Freesurfer community, > > I was trying to use mris_label2annot to generate annotation file, my > commands are: > > mris_label2annot --s p6 --h

[Freesurfer] mris_label2annot gives wrong label

External Email - Use Caution Hi Freesurfer community, I was trying to use mris_label2annot to generate annotation file, my commands are: mris_label2annot --s p6 --h rh --a t500 --ldir $SUBJECTS_DIR/p6/label/regenerated_rh_500 --nhits nhits.mgh --ctab /home/rachelsun/Software/fr

Re: [Freesurfer] mris_label2annot empty Annot

uot;iso-8859-1" > > Dear Freesurfers, > > I am trying to obtain clusters of vertices whit a certain value > over a threshold inside a lesion mask projected to the surface, > with the command: > > > mri_surfcluster --subject MS075_R01_07_R1year --hemi lh --i

Re: [Freesurfer] mris_label2annot empty Annot

; > Dear Freesurfers, > > I am trying to obtain clusters of vertices whit a certain value over a > threshold inside a lesion mask projected to the surface, with the command: > > > mri_surfcluster --subject MS075_R01_07_R1year --hemi lh --in > lh.MS075_R01_07_R1year.subjspace.mgh --surf lh.pial --mas

Re: [Freesurfer] mris_label2annot empty Annot

Can you send the terminal output? On 5/20/19 8:51 AM, Michal Tanzer wrote: > > External Email - Use Caution > > Dear Freesurfer experts, > I am having some difficulties in creating annot file for specific ROIs > using the 2009atlas. When I am using this command, it saves the annot > but

[Freesurfer] mris_label2annot empty Annot

External Email - Use Caution Dear Freesurfer experts, I am having some difficulties in creating annot file for specific ROIs using the 2009atlas. When I am using this command, it saves the annot but I am getting empty files. Using the same command with the aparc.annot file and diff

Re: [Freesurfer] mris_label2annot not creating annot file

Thanks the problem is resolved now. From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Das S. [sarbani@soton.ac.uk] Sent: 21 April 2017 15:47 To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer

[Freesurfer] mris_label2annot not creating annot file

Hi, I was using the mris_label2annot to create .annot file before but now couldn't figure out why the .annot file is not being created. The mris_label2annot is giving the below output but not creating the label files. My label file names are as node-lh-xx.label and the content of ctab file as b

Re: [Freesurfer] mris_label2annot

Hi Caroline the colortables are in $FREESURFER_HOME. Usually we use $FREESURFER_HOME/FreeSurferColorLUT.txt cheers Bruce On Mon, 1 Aug 2016, Caroline Beelen wrote: Dear FS,   Sorry to bother again, but I’m currently in need for some quick help. Today, I also ran into another problem. I

[Freesurfer] mris_label2annot

Dear FS, Sorry to bother again, but I'm currently in need for some quick help. Today, I also ran into another problem. I tried to display only few ROI's in Freeview instead of the whole brain. Therefore, I tried to create a new annotation file consisting of only few labels (from regions of DK-at

Re: [Freesurfer] mris_label2annot & CLUT error

Instead of using an echo this time, I inputted the direct paths straight into the command line. I am in the tcsh shell. On Thu, Sep 10, 2015 at 10:25 AM, Bruce Fischl wrote: > did you try putting an echo in front to see how it expands? What shell are > you using? > > On Thu, 10 Sep 2015, Sam Zor

Re: [Freesurfer] mris_label2annot & CLUT error

did you try putting an echo in front to see how it expands? What shell are you using? On Thu, 10 Sep 2015, Sam Zorowitz wrote: Hi Bruce, Thank you for the reply. I had been running it through python. After running the command from the command line, however, I am still receiving the same error.

Re: [Freesurfer] mris_label2annot & CLUT error

Hi Bruce, Thank you for the reply. I had been running it through python. After running the command from the command line, however, I am still receiving the same error. Best, Sam On Thu, Sep 10, 2015 at 9:00 AM, Bruce Fischl wrote: > Hi Sam > > are you running this from a unix/linux command lin

Re: [Freesurfer] mris_label2annot & CLUT error

Hi Sam are you running this from a unix/linux command line? The >> usually means matlab. In any case, it looks like $CTAB is not being expanded by the shell. Try using echo to see what the actual command is. cheers Bruce On Thu, 10 Sep 2015, Sam Zorowitz wrote: > Hi all, > > I am trying to

[Freesurfer] mris_label2annot & CLUT error

Hi all, I am trying to make a custom annotation file. In doing so, I have created a custom color lookup table. I have attached the CLUT. I run the following command: >> mris_label2annot --subject $SUBJ --hemi $HEMI --ctab $CTAB --a $OUT --l label_1 --l label_2 ... --l label_n And I receive the f

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 > mailto:

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 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 --

Re: [Freesurfer] mris_label2annot: surf/rh.orig No such file or directory

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] mris_label2annot: surf/rh.orig No such file or directory

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 environm

Re: [Freesurfer] mris_label2annot mislabeling

thank you, doug! i was hung up on the names of the .label files when all that matters is the order of the labels in the lookup table. i should have figured that one out! cheers, @rno On Sun, Jun 24, 2012 at 3:50 PM, Douglas N Greve wrote: > what was your command line? Can you send your color

Re: [Freesurfer] mris_label2annot mislabeling

what was your command line? Can you send your color table? It will assign the first label to the first entry in the color table. On 06/24/2012 11:43 AM, Arno Klein wrote: > > yes, but i am confused as to how mris_label2annot uses the color > table. according to > http://surfer.nmr.mgh.harvard.

Re: [Freesurfer] mris_label2annot mislabeling

yes, but i am confused as to how mris_label2annot uses the color table. according to http://surfer.nmr.mgh.harvard.edu/fswiki/LabelsClutsAnnotationFiles, each .label file contains columns of vertex numbers, coordinate values, and a column of zeros. i assume that mris_label2annot assigns the coord

Re: [Freesurfer] mris_label2annot mislabeling

color table, what do i assign for the different anatomical names and color values? why wouldn't the names and colors in FreeSurferColorLUT.txt work? cheers, @rno Re: [Freesurfer] mris_label2annot mislabeling Douglas N Greve Wed, 20 Jun 2012 08:58:50 -0700 Arno, you need to creat

Re: [Freesurfer] mris_label2annot mislabeling

Arno, you need to create a custom color table (--ctab). doug On 06/20/2012 12:05 AM, Arno Klein wrote: > > hello! > > i have saved a couple of .label files and am trying to convert them to > a .annot file with: > > mris_label2annot --h lh --s MMRR-21-1 > --l lh.superiorfrontal.label > --l lh.su

[Freesurfer] mris_label2annot mislabeling

hello! i have saved a couple of .label files and am trying to convert them to a .annot file with: mris_label2annot --h lh --s MMRR-21-1 --l lh.superiorfrontal.label --l lh.superiorparietal.label --ctab FreeSurferColorLUT.txt --a output the stdout is: ColorTable atlas_colortable.txt AnnotName