Re: [Freesurfer] aparcstats2table & asegstats2table version differences

2024-11-12 Thread Douglas N. Greve
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

Re: [Freesurfer] aparcstats2table - append option

2023-12-18 Thread Horn, Mitchell Jacob
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

2023-12-18 Thread Huang, Yujing
...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Huang, Yujing Sent: Monday, December 18, 2023 8:55 AM To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] aparcstats2table - append option I would like to conf

Re: [Freesurfer] aparcstats2table - append option

2023-12-18 Thread Siegel-Ramsay, Jennifer
External Email - Use Caution Unsubscribe Get Outlook for Android

Re: [Freesurfer] aparcstats2table - append option

2023-12-18 Thread Horn, Mitchell Jacob
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

2023-12-18 Thread Huang, Yujing
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 appended to the end of file Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf O

Re: [Freesurfer] aparcstats2table - IndexError

2023-12-15 Thread Huang, Yujing
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 Ext

Re: [Freesurfer] aparcstats2table segmentation fault error

2022-11-20 Thread fsbuild
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

2022-11-20 Thread Eric Yin
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

2022-11-15 Thread fsbuild
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

2022-10-24 Thread Douglas N. Greve
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

Re: [Freesurfer] aparcstats2table {Disarmed}

2020-11-04 Thread Kiyotaka Nemoto
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

Re: [Freesurfer] aparcstats2table error

2020-07-15 Thread Rovai Antonin
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

2020-02-27 Thread Douglas N. Greve
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

2020-02-24 Thread Devika K
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

2020-01-19 Thread Hoopes, Andrew
: 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

2020-01-19 Thread Bruce Fischl
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

2019-05-14 Thread Greve, Douglas N.,Ph.D.
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

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

2018-11-07 Thread Greve, Douglas N.,Ph.D.
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 .

Re: [Freesurfer] aparcstats2table for white surface total area

2018-04-26 Thread Douglas N. Greve
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

Re: [Freesurfer] aparcstats2table subject space?

2018-02-15 Thread Douglas N Greve
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

Re: [Freesurfer] aparcstats2table

2018-01-18 Thread Douglas Greve
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

Re: [Freesurfer] aparcstats2table surface area

2017-10-24 Thread Douglas Greve
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

Re: [Freesurfer] aparcstats2table

2016-11-10 Thread Douglas N Greve
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

2016-11-09 Thread Martin Juneja
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

2016-11-09 Thread Douglas N Greve
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

2016-11-09 Thread Martin Juneja
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

2016-11-09 Thread Douglas Greve
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

Re: [Freesurfer] aparcstats2table -- extracting multiple measures

2015-11-16 Thread Eryilmaz, H. Hamdi
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

2015-11-16 Thread Douglas N Greve
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

2015-11-16 Thread Eryilmaz, H. Hamdi
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

2015-11-13 Thread Douglas Greve
; 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

2015-11-12 Thread Eryilmaz, H. Hamdi
[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

2015-11-12 Thread Douglas N Greve
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

Re: [Freesurfer] aparcstats2table

2015-11-05 Thread Douglas N Greve
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

Re: [Freesurfer] Aparcstats2table Insula Thickness is Zero

2015-09-28 Thread Douglas Greve
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

Re: [Freesurfer] aparcstats2table for functional overlay

2014-05-19 Thread Douglas N Greve
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

Re: [Freesurfer] aparcstats2table for multiple labels

2013-11-11 Thread Douglas Greve
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

2013-11-11 Thread Douglas Greve
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,

Re: [Freesurfer] aparcstats2table error

2013-10-17 Thread Douglas Greve
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

Re: [Freesurfer] aparcstats2table for manually drawn ROIs

2013-10-03 Thread Jackie Lam
Hi Tara, Brilliant, that's exactly what I need. For some reason I was under the impression that the --parc flag was restricted to either the Killiany/Desikan atlas or the Destrieux atlas. Thanks again! Jack On 2013-10-03, at 2:03 PM, Tara Ann Miskovich wrote: > Hi Jack, > > You can specify

Re: [Freesurfer] aparcstats2table for manually drawn ROIs

2013-10-03 Thread Tara Ann Miskovich
Hi Jack, You can specify the .stats file created. Here is an example from the script I use. Anyone, correct me if this is wrong! Tara mris_anatomical_stats -l ${subject}/label/lh.frontalmerge.label -f ${subject}/stats/lh_frontal_surface.stats ${subject} lh pial aparcstats2table --hemi lh \ -

Re: [Freesurfer] aparcstats2table error

2011-02-25 Thread Douglas N Greve
; 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

2011-02-25 Thread Alex Hanganu
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

2011-02-24 Thread Chris Hyatt
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

2011-02-24 Thread Douglas N Greve
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 --

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

2010-01-11 Thread Douglas N Greve
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

RE: [Freesurfer] aparcstats2table

2009-04-14 Thread Falk Lüsebrink
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

2009-04-14 Thread Krish Subramaniam
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/

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

2009-02-06 Thread Diana Wotruba
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)

2009-02-06 Thread Pratap Kunwar
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,

Re: [Freesurfer] aparcstats2table bug

2009-02-05 Thread Krish Subramaniam
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

2009-02-05 Thread Krish Subramaniam
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

2009-02-05 Thread Douglas N Greve
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

2009-02-05 Thread Krish Subramaniam
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