Re: [Freesurfer] aparcstats2table & asegstats2table version differences

It is certainly fixed in 7x version. I think it is fixed in the patch per the documentation On 11/7/2024 3:41 PM, Heffernan, Zachary wrote: External Email - Use Caution Hello FreeSurfer Mailing List, I see in the Release Notes

[Freesurfer] aparcstats2table & asegstats2table version differences

External Email - Use Caution Hello FreeSurfer Mailing List, I see in the Release Notes

Re: [Freesurfer] aparcstats2table - append option

Wow that was fast! Thanks! -Mitch From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Huang, Yujing Sent: Monday, December 18, 2023 2:18:19 PM To: Freesurfer support list Subject: Re: [Freesurfer] aparcstats2table - append option '--append'

Re: [Freesurfer] aparcstats2table - append option

ubject: Re: [Freesurfer] aparcstats2table - append option Exactly. My understanding (and correct me if I'm wrong) is that both commands create/overwrite the specified --tablefile each time it's run. Best, Mitch From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun

Re: [Freesurfer] aparcstats2table - append option

tchell Jacob Sent: Tuesday, December 12, 2023 9:10:22 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] aparcstats2table - append option Hi FS Devs, Would it be possible to add an “append” flag for use with aparcstats2table and asegstats2table? If I understand their usage correctly

Re: [Freesurfer] aparcstats2table - append option

er support list Subject: Re: [Freesurfer] aparcstats2table - append option I would like to confirm that this is what you have in mind: 1. the new '-append' flag will work with '--tablefile=OUTPUTFILE' 2. when same OUTPUTFILE is specified, new stats output will be appe

Re: [Freesurfer] aparcstats2table - append option

vard.edu On Behalf Of Horn, Mitchell Jacob Sent: Tuesday, December 12, 2023 10:10 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] aparcstats2table - append option Hi FS Devs, Would it be possible to add an "append" flag for use with aparcstats2table and asegstats2tabl

Re: [Freesurfer] aparcstats2table - IndexError

Can you check if you have any extra empty lines after your last ‘Input’? From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Laura Willers de Souza Sent: Thursday, December 14, 2023 3:16 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] aparcstats2table - IndexError

[Freesurfer] aparcstats2table - IndexError

External Email - Use Caution Hello FreeSurfer Developers, I'm trying to get the cortical thickness values for a list of subjects using aparcstats2table and I'm encountering this error: aparcstats2table --fsgd subjects.test1.fsgd --meas thickness --hemi lh --common-parcs --table

[Freesurfer] aparcstats2table - append option

Hi FS Devs, Would it be possible to add an "append" flag for use with aparcstats2table and asegstats2table? If I understand their usage correctly, each time one of them are run they will create (or overwrite) a new file. Not urgent but would be useful. Thanks, Mitch ___

Re: [Freesurfer] aparcstats2table segmentation fault error

External Email - Use Caution You don’t need to manually set MINC_BIN_DIR or the MINC_LIB_DIR variables as those should get set when you source the freesurfer setup script. Try manually running the bash shell, set FREESURFER_HOME, and check you can see that directory, $ bash$ expo

Re: [Freesurfer] aparcstats2table segmentation fault error

better. From: fsbuild<mailto:fsbu...@contbay.com> Sent: November 15, 2022 10:07 PM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Cc: Eric Yin<mailto:eric@mail.utoronto.ca> Subject: Re: [Freesurfer] aparcstats2table segmentation fault error You don

Re: [Freesurfer] aparcstats2table segmentation fault error

External Email - Use Caution Difficult to enlarge your screenshots and read the text, but it looks like even though the output from the setup script displays the path to FREESSURFER_HOME, the script wrapper for the shell cannot verify that path actually exists.   And it looks li

Re: [Freesurfer] aparcstats2table command

See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/AnatomicalROI instead of listing all the subjects on the command line, put all the subjects names in a file and use --subjectsfile=SUBJECTSFILE On 10/20/2022 12:03 PM, eso wrote: External Email - Use Caution Hi Freesurfer expe

[Freesurfer] aparcstats2table command

External Email - Use Caution Hi Freesurfer experts, I am new to the Freesurfer world ! My question is how to use aparcstats2table to extract data for a large number of subjects (approximately 700 subjects). I have tried to paste the folder path that included all the pre-proces

[Freesurfer] aparcstats2table

External Email - Use Caution hi I run in linux command: """ aparcstats2table --hemi lh --subjects /home/team33/MRI4/subj10/stats --parc aparc.a2009s --meas meancurv --tablefile /home/team33/ aparcstats .txt """

Re: [Freesurfer] aparcstats2table {Disarmed}

External Email - Use Caution Hi, Suppose the fsid of your subj10 is subj10 and you set SUBJECTS_DIR correctly to /home/team33/MRI4, the command should be aparcstats2table --hemi lh --subjects subj10 --parc aparc.a2009s --meas meancurv --tablefile /home/team33/aparcstats.txt I

[Freesurfer] aparcstats2table

External Email - Use Caution hi I run in linux command:""" aparcstats2table --hemi lh  --subjects /home/team33/MRI4/subj10/stats --parc aparc.a2009s  --meas meancurv --tablefile /home/team33/ aparcstats.txt"

Re: [Freesurfer] aparcstats2table error

mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Sunday, January 19, 2020 at 9:09 AM To: FS Help mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] aparcstats2table error External Email - Use Caution I tried doing cortical parcellation using Destrieux atlas. I ran

Re: [Freesurfer] aparcstats2table

yes On 2/25/20 2:05 AM, Devika K wrote: > > External Email - Use Caution > > Hi, > > Can I use the below command to extract the cortical thickness using > Destrieux Atlas from longitudinally preprocessed subjects? > aparcstats2table --hemi lh \ >--subjects 004 021 040 067 080 092 \ >

Re: [Freesurfer] aparcstats2table

External Email - Use Caution Hi, Can I use the below command to extract the cortical thickness using Destrieux Atlas from longitudinally preprocessed subjects? aparcstats2table --hemi lh \ --subjects 004 021 040 067 080 092 \ --meas thickness \ --parc aparc.a2009s \ --tab

Re: [Freesurfer] aparcstats2table error

: on behalf of Devika K Reply-To: FS Help Date: Sunday, January 19, 2020 at 9:09 AM To: FS Help Subject: Re: [Freesurfer] aparcstats2table error External Email - Use Caution I tried doing cortical parcellation using Destrieux atlas. I ran the aparcstats2table command from the

Re: [Freesurfer] aparcstats2table error

Hi Devika In the future can you include the text of the command and the output in your email instead of a screenshot? That will make our job easier. Try specifying which subjects you want processed explicitly with --subjects cheers Bruce On Sun, 19 Jan 2020, Devika K wrote: Ex

Re: [Freesurfer] aparcstats2table

I can't replicate the error (even when using the same subject name), so I'm not sure what to say. The only think I can think of is that it is something in your environment that is causing the strangeness. Can someone you work with run the command to see if the same error happens? On 5/14/19 5:0

[Freesurfer] aparcstats2table

External Email - Use Caution Hi Doug: I used the following command: [airhunger:Structural_for_7T] (nmr-stable6-env) aparcstats2table --subjects 100610 --hemi rh --meas thickness --tablefile aparc_stats.txt However, I got an error message: File "/usr/local/freesurfer/stable6/b

Re: [Freesurfer] aparcstats2table --parcs-from-file trouble

If you are using output froom mri_segstats, then you need to use asegstats2table, not aparcstats2table. It can be confusing ... On 11/01/2018 05:06 PM, Figueiro Longo, Maria Gabriela wrote: > > Hi, > > > I extracted some volumes using mri_annotation2lable --> mri_aparc2aseg > --> mri_segstats .

[Freesurfer] aparcstats2table --parcs-from-file trouble

Hi, I extracted some volumes using mri_annotation2lable --> mri_aparc2aseg --> mri_segstats . Now I am trying to extract the summary table using aparcstats2table --parcs-from-file , but every time an error message pops up: ERROR: cannot read The stats files generated by the mri_segstats l

Re: [Freesurfer] aparcstats2table for white surface total area

If you just run aparcstats2table it should be in the table. I don't think there is a way to only get that value On 04/26/2018 11:20 AM, Sian Emma Davies wrote: > > External Email - Use Caution > > Hello, > > Forgive me, I’m new to FreeSurfer. I wish to collate values of white > surface

[Freesurfer] aparcstats2table for white surface total area

External Email - Use Caution Hello, Forgive me, I'm new to FreeSurfer. I wish to collate values of white surface total area from all my subjects into a single table, so that I can control for this in my analyses. I understand this value is in the aparc.stats files for each part

Re: [Freesurfer] aparcstats2table subject space?

Yes, it is in native subject space On 02/07/2018 07:35 AM, Kasper Jessen wrote: > > Dear FreeSurfer, > > When you extract e.g. thickness from the command aparcstats2table – is > the data extracted from subject space? > > We need to know whether or not, we need to covariate for total brain > vol

[Freesurfer] aparcstats2table subject space?

Dear FreeSurfer, When you extract e.g. thickness from the command aparcstats2table - is the data extracted from subject space? We need to know whether or not, we need to covariate for total brain volume. Bw Kasper Kasper Jessen, MD, PhD student Center for Neuropsychiatric Schizophrenia Researc

Re: [Freesurfer] aparcstats2table

Why don't you just create a fake directory structure. Should be pretty easy to script (if you know how to script:) On 1/15/18 3:44 AM, Stephanos Leandrou wrote: Dear Freesurfer Developers, I want to use the asegstats2table and aparcstats2table for my research. First of all, my subjects (sev

[Freesurfer] aparcstats2table

Dear Freesurfer Developers, I want to use the asegstats2table and aparcstats2table for my research. First of all, my subjects (several hundreds) are not in the Freesurfer/Subjects directory and for each one I have run the recon-all command. For the asegstats2table command we know that the subje

Re: [Freesurfer] aparcstats2table surface area

On 10/24/17 2:37 AM, Kasper Jessen wrote: Hi FreeSurfer, We have extracted the surface area using aparcstats2table. 1.The ROIs extracted are by default the White Surface Area, correct? Correct. 2.Why does the WhiteSurfArea (default average) have decimals but not the surface area of the

[Freesurfer] aparcstats2table surface area

Hi FreeSurfer, We have extracted the surface area using aparcstats2table. 1.The ROIs extracted are by default the White Surface Area, correct? 2.Why does the WhiteSurfArea (default average) have decimals but not the surface area of the different ROIs? When taking the SUM of all the RO

Re: [Freesurfer] aparcstats2table

This appears to be broken in 5.3. You can do 2 things: (1) specify the subjects in a different way, or (2) use the aparcstats2table below. I'm not 100% sure it will work in the 5.3 env, so make a backup of your aparcstats2table file. https://gate.nmr.mgh.harvard.edu/safelinks/greve/aparcstats2t

Re: [Freesurfer] aparcstats2table

Hi Dr. Greve, Please find the attached qdec file, along with diagnosis file which I used in QDEC, and this is the same qdec file I trying to use for the aparcstats2table command. Thanks. PS: I was also wondering (a) how can I average thickness stats (b) are these in fsaverage (standard) space an

Re: [Freesurfer] aparcstats2table

can you send the qdec file with variables? On 11/09/2016 11:51 AM, Martin Juneja wrote: > Hi Dr. Greve, > > Somehow even after adding variables, it's not working, although same > qdec file works fine when I perform GLM in qdec. > So I replaced the flag with subjectsfile and provided subject list

Re: [Freesurfer] aparcstats2table

Hi Dr. Greve, Somehow even after adding variables, it's not working, although same qdec file works fine when I perform GLM in qdec. So I replaced the flag with subjectsfile and provided subject list.txt file. So in that way, it's working fine now. I was also wondering (a) how can I average these

Re: [Freesurfer] aparcstats2table

Appears to be having problems reading the qdec table. It might be expecting the qdec table to actually variables in it. Can you try adding variables? Also, try it without the --qdec flag instead specifying the subjects with --subjects HC003_1 HC004_1 ... On 11/8/16 8:09 PM, Martin Juneja wrot

[Freesurfer] aparcstats2table

Hi everyone, I am trying to use following command to save stats from a set of subjects in a table format: aparcstats2table --qdec qdec.dat --hemi lh --meas thickness -t zzz.txt But after I run this, I get following error: Traceback (most recent call last): File "/usr/local/freesurfer/bin/apa

Re: [Freesurfer] aparcstats2table -- extracting multiple measures

2:28 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] aparcstats2table -- extracting multiple measures what version of FS are you using? When I run aparcstats2table --hemi lh -s subject --meas foldind --tablefile table.dat it runs fine On 11/16/2015 10:24 AM, Eryilmaz, H. Hamdi wrote:

Re: [Freesurfer] aparcstats2table -- extracting multiple measures

t; > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Friday, November 13, 2015 6:27 PM > To: freesurfer@nmr.mgh.harvard.edu > Sub

Re: [Freesurfer] aparcstats2table -- extracting multiple measures

ipt to extract it? Thanks! Hamdi From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas Greve [gr...@nmr.mgh.harvard.edu] Sent: Friday, November 13, 2015 6:27 PM To: freesurfer@nmr.mgh.harvard.edu Subjec

Re: [Freesurfer] aparcstats2table -- extracting multiple measures

; Best, > Hamdi > > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve > [gr...@nmr.mgh.harvard.edu] > Sent: Thursday, November 12, 2015 11:26 AM > To: freesurfer@nmr.mgh.harvard.edu &g

Re: [Freesurfer] aparcstats2table -- extracting multiple measures

[freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Douglas N Greve [gr...@nmr.mgh.harvard.edu] Sent: Thursday, November 12, 2015 11:26 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] aparcstats2table -- extracting multiple measures you have to run it separately On 11/12/2015 11:18 AM

Re: [Freesurfer] aparcstats2table -- extracting multiple measures

you have to run it separately On 11/12/2015 11:18 AM, Eryilmaz, H. Hamdi wrote: > Dear experts, > > I am using aparcstats2table to extract values on a number of measures > like thickness, curvature, folding index, and surface area for > specific ROIs. Is it possible to create a table (using > a

[Freesurfer] aparcstats2table -- extracting multiple measures

Dear experts, I am using aparcstats2table to extract values on a number of measures like thickness, curvature, folding index, and surface area for specific ROIs. Is it possible to create a table (using aparcstats2table) with all these measures included or do I have to run it separately and cre

Re: [Freesurfer] aparcstats2table

white On 11/05/2015 04:18 PM, Yang, Daniel wrote: > Dear FreeSurfer Experts, > > When I perform aparcstats2table —meas area, does it get it pial.area > or white area? > > I believe it is the pial.area, but this is not documented. If yes, > what can I obtain white area via aparcstats2table? > > T

[Freesurfer] aparcstats2table

Dear FreeSurfer Experts, When I perform aparcstats2table —meas area, does it get it pial.area or white area? I believe it is the pial.area, but this is not documented. If yes, what can I obtain white area via aparcstats2table? Thanks, Daniel -- Daniel Yang, Ph.D. Yale Child Study Center E-mai

Re: [Freesurfer] Aparcstats2table Insula Thickness is Zero

Can you send the command and terminal output? On 9/24/15 2:23 PM, Popal, Haroon (NIH/NIMH) [F] wrote: Hello, When I use aparcstats2table to pull thickness values of the Desikan atlas, I get a value of zero for two of my subject’s insula thickness in both hemispheres. For these two subjects, I

[Freesurfer] Aparcstats2table Insula Thickness is Zero

Hello, When I use aparcstats2table to pull thickness values of the Desikan atlas, I get a value of zero for two of my subject’s insula thickness in both hemispheres. For these two subjects, I also get values for “lh_unknown_thickness” and “lh_corpuscallosum_thickness”, while all of the other s

Re: [Freesurfer] aparcstats2table for functional overlay

You can use mri_segstats to create a stats file which averages the data over an ROI (you can pass it an annotation). If you do this for each individual, you then run asegstats2table passing it each of the individual tables (don't be fooled by the name of asegstats2table, it is just the program

[Freesurfer] aparcstats2table for functional overlay

Hi all, I was wondering if there was a script like aparcstats2table that would accept a functional overlay file that has been sampled to the surface as a measure instead of the available options for structural measures? In tksurfer there is a manual way to average over an ROI using the sig.mgh an

Re: [Freesurfer] aparcstats2table for multiple labels

The only way to do what you want is to combine the labels into an annotation file (mris_label2annot), then run mris_anatomical_stats on the annot, then you can run aparcstats2table on the output of that. This may or may not be easier than doing what you are already doing. doug. On 11/10/13 3:

Re: [Freesurfer] aparcstats2table question

I think you just need the qdec table. doug On 11/11/13 11:27 AM, Jonathan Holt wrote: > Hi FS experts, > > I’m about to run aparcstats2table for a longitudinal study, and I’m wondering > seeing as I’ve already written a longitudinal qdec table that includes > subject IDs under the fsid column,

[Freesurfer] aparcstats2table question

Hi FS experts, I’m about to run aparcstats2table for a longitudinal study, and I’m wondering seeing as I’ve already written a longitudinal qdec table that includes subject IDs under the fsid column, is it necessary to pass -subjects subj1 subj2 subj3 … etc AND the qdec to aparcstats2table or sh

[Freesurfer] aparcstats2table for multiple labels

Dear fs experts, I have created 5 customized labels that I want to extract mean thickness from each subject. Is there a way to generate a text file for all the labels I made? For example, aparcstats2table --parc option only allows to read one label at a time. I am wondering if there is a way for

Re: [Freesurfer] aparcstats2table error

Hi Corinna, is it just that subject or does it happen on more? Can you send me the stats file? doug On 10/17/13 3:55 PM, Corinna Bauer wrote: Hi; I want to put cortical thickness in a table format and am getting an error. command: aparcstats2table --subjectsfile symmetry_subjects.txt --he

[Freesurfer] aparcstats2table error

Hi; I want to put cortical thickness in a table format and am getting an error. command: aparcstats2table --subjectsfile symmetry_subjects.txt --hemi lh --meas thickness --tablefile symm_aparc_stats_rh.txt error: ERROR: The stats file /media/working_tb_drive/symmetry/MMT_08292013/stats/lh.aparc.s

Re: [Freesurfer] aparcstats2table for manually drawn ROIs

h pial > > aparcstats2table --hemi lh \ > --subjects sub1 sub2 sub3 \ > --meas thickness \ > --parc lh_frontal_surface \ > --tablefile lh.frontal_thickness.stats.txt > > > - Original Message - > From: "Jackie Lam" > To: freesurfer@nmr.mgh

Re: [Freesurfer] aparcstats2table for manually drawn ROIs

\ --subjects sub1 sub2 sub3 \ --meas thickness \ --parc lh_frontal_surface \ --tablefile lh.frontal_thickness.stats.txt - Original Message - From: "Jackie Lam" To: freesurfer@nmr.mgh.harvard.edu Sent: Thursday, October 3, 2013 12:51:21 PM Subject: [Freesurfer] aparcstats

[Freesurfer] aparcstats2table for manually drawn ROIs

Hi there, So I've run recon-all on my group of subjects, ran them in QDEC, manually drawn my ROIs, used mris_anatomical_stats to create a .stats files for each subject from my hand drawn ROIs and now I want to use aparcstats2table to gather the thicknesses from all my subjects Is there an o

Re: [Freesurfer] aparcstats2table error

; in the address. > > Doug - > Thanks, mris_anatomical_stats works. For this it was also necessary to > copy the .label file in each subjects - "/label/" directory > > > Alex > > --- En date de : *Jeu 24.2.11, Chris Hyatt //* a > écrit : > > > De: Chris Hyatt &

Re: [Freesurfer] aparcstats2table error

écrit : De: Chris Hyatt Objet: Re: [Freesurfer] aparcstats2table error À: "FS Mailing List" , "Alex Hanganu" Date: Jeudi 24 février 2011, 18h48 You have /stat/ rather than /stats/ in the address. Have you checked that? >>> Alex Hanganu 2/24/2011 12:22 PM >>&g

Re: [Freesurfer] aparcstats2table error

You have /stat/ rather than /stats/ in the address. Have you checked that? >>> Alex Hanganu 2/24/2011 12:22 PM >>> Dear Chris, Doug, We created a ROI in qdec (EXMPL.label) and tried to measure it's thickness. The cmd used: aparcstats2table --hemi ?h --subjects 1 2 3 --parc .../DIR/EXMPL.label

Re: [Freesurfer] aparcstats2table error

Use mris_anatomical_stats. aparcstats2table is used for combining several outputs of mris_anatomical_stats. Alex Hanganu wrote: > Dear Chris, Doug, > > We created a ROI in qdec (EXMPL.label) and tried to measure it's > thickness. > > The cmd used: > aparcstats2table --hemi ?h --subjects 1 2 3 --

[Freesurfer] aparcstats2table error

Dear Chris, Doug, We created a ROI in qdec (EXMPL.label) and tried to measure it's thickness. The cmd used: aparcstats2table --hemi ?h --subjects 1 2 3 --parc .../DIR/EXMPL.label --meas thickness --t ROI.txt ERROR: cannot find .../freesurfer/subjects/SUBJECT_NAME/stat/EXMPL.label.statsqdec/DIR

Re: [Freesurfer] aparcstats2table for std dev associated with av thickness

I've modified aparc2stats2table to accept a -meas thicknessstd option. This will output the spatial standard deviation of the thickness for each subject. You can get it from here: ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/aparcstats2table doug Ritobrato Datta wrote: > Hi al

[Freesurfer] aparcstats2table for std dev associated with av thickness

Hi all Is there a way to create a multi subject table of the std dev associated with av thickness using aparcstats2table or for that matter any way to create a table similar to the outout of aparcstats2table ? Thanks Ri ___ Freesurfer mailing list Fr

RE: [Freesurfer] aparcstats2table

Subject: Re: [Freesurfer] aparcstats2table Hi Falk fsutils is one of the 4 helper scripts missing from the distribution. Please get the 4 scripts from here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/fixes/datastruct_utils. py ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/fixes

Re: [Freesurfer] aparcstats2table

Hi Falk fsutils is one of the 4 helper scripts missing from the distribution. Please get the 4 scripts from here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/fixes/datastruct_utils.py ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/fixes/fsutils.py ftp://surfer.nmr.mgh.harvard.edu/

[Freesurfer] aparcstats2table

Hi Freesurfers, I tried using aparcstats2table today and encountered following error message: Trackback (most recent call last): File “usr/share/freesurfer/bin/aparcstats2table”, line 6, in Import fsutils ImportError: No module named fsutils Is anyone able to offer some help?

Re: [Freesurfer] aparcstats2table new version (-parc)

Dear Pratap The file is called ?h.aparc.a2005s_300.stats as you suggested. The commands I used are the following: mris_divide_parcellation fsaverage_fineparc ?h aparc.a2005s.annot 300 ?h.aparc.a2005s_300.annot mri_surf2surf --srcsubject fsaverage_fineparc --sval-annot aparc.a2005s_300.anno

Re: [Freesurfer] aparcstats2table new version (-parc)

Hi Diana, Make sure you name stats file as ?h.aparc.a2005s_300.stats not just aparc.a2005s_300.stats. then --parc aparc.a2005s_300 this should work otherwise if you post your commands, that will help. thanks pratap > > Hi Krish > > Thanks again for your quick help! I tried out the new version,

[Freesurfer] aparcstats2table new version (-parc)

Hi Krish Thanks again for your quick help! I tried out the new version, it seams to work fine. Nevertheless, I created a new parcellation with mris_anatomical_stats getting a .stat file I called aparc.a2005s_300. Only now I get the following error message (Which was not the case in the f

Re: [Freesurfer] aparcstats2table bug

Hi Diana I have put the latest rewrite ( more fixes and updates ) of both the aparcstats2table and asegstats2table here. If you still haven't tried with the previous one we sent you, use this version instead. ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/fixes/stats2table.tar.gz Ext

Re: [Freesurfer] aparcstats2table bug

Hi Diana I've put it here. ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/fsdev/krish/stats2table_alpha.tar.gz To install cp stats2table_alpha.tar.gz $FREESURFER_HOME/bin/ cd $FREESURFER_HOME/bin tar zvxf stats2table_alpha.tar.gz The binary is named "aparcstats2table_re" ( _re for rewrite

Re: [Freesurfer] aparcstats2table bug

Krish actually has a new version and is looking for alpha testers Krish, do you want to give Diana a copy? doug Diana Wotruba wrote: Dear experts If some of the subjects in a group have missing values of a certain label, aparcstats2table fails to designate a 0 for them. According to

Re: [Freesurfer] aparcstats2table bug

We have done a rewrite of both aparcstats2table and asegstats2table, although it needs a little a bit of testing, still. I'll put the new version online and send you the link soon. It will be great if you can test i) the bug in question and ii) aparcstats2table in general. Both will definit

[Freesurfer] aparcstats2table bug

Dear experts If some of the subjects in a group have missing values of a certain label, aparcstats2table fails to designate a 0 for them. According to the freesurfers website, this bug will be fixed in the next release. Is it already known when this can be expected? Thanks in advance Dian