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That worked!
*python2 /opt/softwarepackages/freesurfer/bin/long_mris_slopes --qdec
qdec/long.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate
--do-pc1 --do-spc --do-stack --do-label --time months --qcache fsaverage
--sd $SUBJECTS_DIR*
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This is a bit of a guess, but I think the issue is that the script requires
python2, but your python interpreter (the 'python' command on your system)
points to python3.
You can check whether this is the case by running:
python --version
If
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Hello, I am trying to do some preliminary analysis of a
longitudinal dataset, following the tutorial.
I am running FS on Ubuntu 20.04 and
freesurfer-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c
I have finished processing the dataset; to prepare
Hi Anwar,
I see, you want to convert the mgh file back to some text table. Not
sure how that worked, but I think mri_convert could do it (but maybe
only for a single subject with several structures, not sure about
multiple subjects - this is a stacked file). Another way is to open the
mgh in
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Hi Martin/Doug:
Still looking for an answer. Could not find a way to list the percentage change
values for each subject in a tabular form.
Thanks,
Anwar
On 2018-08-30, 12:15 PM, "Shatil, Anwar Shahadat"
wrote:
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Hello Martin:
I am using freesurfer 6.0.0 and the long_mris_slopes version 1.42 (that came
with it by default).
If I omit --out-pc1 but keep --do-pc1 still do not get any output as a .dat or
.stats file. I only get .mgh file in surf folder.
I need
Hi Anwar,
what FS version are you using?
Also what happens if you omit the --out-pc1 but keep the --do-pc1 ?
Also no output with that ending? It should write it to the default
location.
Best, Martin
On Wed, 2018-08-29 at 16:45 +, Shatil, Anwar Shahadat wrote:
> External Email
External Email - Use Caution
?Dear Doug:
I am trying to get a table containing pc1 values for each subject in a
longitudinal study and failed to extract this. I use the code below:
long_mris_slopes --qdec ./qdec/long.qdec.table.2.dat --meas thickness --hemi lh
--do-avg
Hi Carolina,
probably you are not interested in the average thickness, so you can
drop --do-avg . Also usually people decide between pc1 and spc. The
stack is also not really necessary unless you want to look at it.
Try to remove the trailing / at fsaverage and --sd $SUBJECTS_DIR
that should
Hi FreeSurfer experts,
I am trying to run Longitudinal Two Steps analysis.
In the long_mris_slopes I run the following command:
long_mris_slopes --qdec $SUBJECTS_DIR/qdec/longRRMSP01.qdec.table.dat --meas thickness --hemi lh --do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time
Hi Katherine,
are you sure you downloaded the right executable for your operating
system? It seems to be not able to run the command (exec format error).
Did you replace mri_convert?
what happens if you run the command yourself:
mri_convert --frame 0
Hi Freesurfer experts,
I'm working on analyzing longitudinal data using the longitudinal 2-stage
model. When running the data through long_mris_slopes, I was getting the
following error message: ERROR 1 : mris_calc compute sym. pct. change (spc)
problem?
I saw in previous messages that this is
Hi Vincent,
yes, it is tp2-tp1 / time_delta
so thinning is negative, thickening positive. I'll correct the help
text, the tutorial is right.
It knows about the time point ordering because of the time column.
Best, Martin
On 08/02/2013 09:04 PM, vbrun...@nmr.mgh.harvard.edu wrote:
Dear
Dear Freesurfer experts,
I have followed the LongitudinalTutorial with two time points + two
groups and now, after looking at the output of the qdec analysis, I just
want to make sure I haven't made a sign error as for the control group
the difference is as expected around 0 but for the
: Thu, 20 Jun 2013 06:57:16 -0700
To: bohn-pe...@gmx.de; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found
Not totally sure with 5.0, but I don't think it requires same voxel space for
all time points (since 5.1), so it should work to run
to be an empty line somewhere in the file?
Thanks a lot!
Best regards
Peter
From: bohn-pe...@gmx.de
To: mreu...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu
Date: Mon, 1 Jul 2013 15:32:04 +0200
Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command not found
Dear
Freesurfer
in the file?
Thanks a lot!
Best regards
Peter
From: bohn-pe...@gmx.de
To: mreu...@nmr.mgh.harvard.edu; freesurfer@nmr.mgh.harvard.edu
Date: Mon, 1 Jul 2013 15:32:04 +0200
Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table
@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] long_mris_slopes/cross.qdec.table.dat
Hi Peter,
it needs to be .Qdecrc and have these lines:
MEASURE1 = long.thickness-avg
MEASURE2 = long.thickness-rate
MEASURE3 = long.thickness-pc1
MEASURE4 = long.thickness-spc
You
:39 -0400
From: mreu...@nmr.mgh.harvard.edu
To: bohn-pe...@gmx.de
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] long_mris_slopes/cross.qdec.table.dat
Hi Peter,
it needs to be .Qdecrc and have these lines:
MEASURE1 = long.thickness-avg
MEASURE2 = long.thickness-rate
MEASURE3
Dear Freesurfer experts,
I was trying to run some longitudinal analysis but whenever I want to use the
commands “long_mris_slopes” or “long_qdec_table” I just get
“command not found” as an answer. When I try to look up a package that might
include the command, by typing “cnf
Hi Peter,
can you run any free surfer command at all? Looks to me that you did not source
free surfer. What happens if you type
freesurfer
into the terminal window? It should print the version.
Best, Martin
On Jun 20, 2013, at 5:17 AM, Peter Bohn bohn-pe...@gmx.de wrote:
Dear
the version’s name. All other commands I use run perfectly
fine.
Thanks once again!
Best regards
Peter
From: mreu...@nmr.mgh.harvard.edu
Date: Thu, 20 Jun 2013 05:21:39 -0400
To: bohn-pe...@gmx.de
CC: freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] long_mris_slopes/long_qdec_table command
Hi Peter
we use semething similar, although we've extended it and made it
significantly more accurate. If you want to contact the CMA you can try:
Dave Kennedy kenn...@nmr.mgh.harvard.edu
cheers
Bruce
On
Thu, 20 Jun 2013, Peter Bohn wrote:
Dear Freesurfer experts,
I was trying to
runs once I use the new version
or are
they compatible concerning this aspect?
Thank you very much!
Best regards
Peter
From: mreu...@nmr.mgh.harvard.edu
Date: Thu, 20 Jun 2013 02:46:05 -0700
To: bohn-pe...@gmx.de; freesurfer@nmr.mgh.harvard.edu
Subject: Re: [Freesurfer] long_mris_slopes
I was able to solve my problem in my earlier email included below. I downloaded
a new verison of mris_calc made it executable with chmod +x FILE and then
replaced it in the bin folder. I included this response in case anyone else
runs into the same problem and does a search.
Hello Freesurfer experts,
I am working on a study that wants to compare pre/post cortical thickness on an
intervention group and a control group. I am using FS 5.1 on a Mac. I have
processed all the recons through the longitudinal stream as described in the
wiki/tutorial. However when I go to
Freesurfer@nmr.mgh.harvard.edu
*Envoyé le :* mercredi 3 octobre 2012 17h30
*Objet :* Re: [Freesurfer] long_mris_slopes error
Not sure.
Maybe try the updated scripts
From
http://martinos.org/~mreuter/long
http://martinos.org/%7Emreuter/long/
Best Martin
Alex Hanganu
,
Best regards,
Alex.
De : Martin Reuter mreu...@nmr.mgh.harvard.edu
À : Alexandru Hanganu al.hang...@yahoo.ca; FS Mailing List
Freesurfer@nmr.mgh.harvard.edu
Envoyé le : mercredi 3 octobre 2012 17h30
Objet : Re: [Freesurfer] long_mris_slopes error
Not sure
@nmr.mgh.harvard.edu
Envoyé le : mercredi 3 octobre 2012 17h30
Objet : Re: [Freesurfer] long_mris_slopes error
Not sure.
Maybe try the updated scripts
From
http://martinos.org/~mreuter/long/
Best Martin
Alex Hanganu al.hang...@yahoo.ca wrote:
Dear Freesurfer Experts,
While performing
Dear Freesurfer Experts,
While performing the long_mris_slopes cmd, we receive an error:
---
SUBJECT pls_pd_base00 Running Within-Subject GLM
Writing ./tmp-pls_pd_base00_lh_thickness_Rx7HLs/X-long.mat ...
mri_glmfit --y
Not sure.
Maybe try the updated scripts
From
http://martinos.org/~mreuter/long/
Best Martin
Alexandru Hanganu al.hang...@yahoo.ca wrote:
Dear Freesurfer Experts,
While performing the long_mris_slopes cmd, we receive an error:
---
SUBJECT pls_pd_base00
Hi Martin,
I am a little confused about these mapped files in the base directories
you are referring to. How would I check them?
-Shannon K.
On Fri, Sep 28, 2012 at 4:08 PM, Martin Reuter
mreu...@nmr.mgh.harvard.eduwrote:
I see,
Usually people look at thickness maps and volume on an ROI
Hi Shannon,
that cannot be. It either indicates a serious bug (which we have not yet
encountered in our data) or a problem with your processing.
Can you send me:
- the version you use
- the command line you run
- the output you get
Also long_mris_slopes is designed for analyzing surface maps
Hi Martin,
I am running FS version 5.1.
This is the command line I ran:
long_mris_slopes --qdec ./qdec/long.qdec.table.dat --meas volume --hemi lh
--do-avg --do-rate --do-pc1 --do-spc --do-stack --do-label --time years
--qcache fsaverage
These are the outputs I get, which are located in the
I see,
Usually people look at thickness maps and volume on an ROI basis. Volume on the
surface I think is simply area times thickness. Not sure how meaningful that is
as area of a vertex depends on the triangle mesh.
Anyway, you look at smoothed maps on fsaverage. The average volume for each
Hi Shannon,
long_mris_slopes works for surface maps (both thickness and volume
should work). In both cases it should compute the temporal average.
I have another scripts that works for stats files (long_stats_slopes) in
the same way.
How many time points do you have, how far apart (equally
Hi,
I had a question about how the temporal average is calculated for subjects
with multiple timepoints. I used the long_mris_slopes command on a
longitudinal set of data. However, when I compared the average volumes
calculated through this command to the average volumes calculated in excel
after
Hi Shannon
You probably mean average thickness.
My scripts compute the temporal average from the linear fit (at mid time),
which can be differed from simply averaging values.
Best Martin
Shannon Kogachi skoga...@gmail.com wrote:
Hi,
I had a question about how the temporal average is calculated
Hi Martin,
When I used the long_mris_slopes command for the thickness, the average
thickness calculated in FreeSurfer was pretty similar to averaging the
values in FreeSurfer. Does this command only work thickness measures and
not for volume or area? Thanks!
-Shannon
On Wed, Sep 26, 2012 at
Hi Hyojeong,
on the wiki release notes is a fixed mris_calc binary.
Best, Martin
On Aug 11, 2011, at 8:00 AM, Administrator wrote:
Dear Martin,
I've received the same error as below which discussed previously.
Would you tell me if you managed build a fixed file, please?
Hyojeong Lee
Hi Derin,
there is a know and fixed bug in mris_calc in the 5.1 release. It has
difficulties with very long file names and returns a non zero exit code,
which stops my script in some situations.
I'll ask Nick if he can put up a fixed version of mris_calc for
download.
Best, Martin
On Thu,
I received the follow error while running a set of subjects under
'long_mris_slopes,' and wasn't able to decipher the problem. It appears that
mris_calc is not able to do the division for these files (dividing by 0
perhaps?). Any help appreciated, here's the command and tail end of
Hi Sean,
symmetrized percent change is a measure across time. for two time points it is
just
100*(tp2-tp1)/(0.5*(tp1+tp2)) (if they are a time unit (usually year) apart,
else we divide by time difference)
You are basically fine. We need to distinguish between processing and
post-processing.
Hi Martin and all,
I would like to ask you if by comparing tp1 thickness-spc with tp2 (and
comparing tp2 with tp3) using the base brain between tp1,2 and 3
(altogether) I have messed up methodologically.
I was expecting a rise in cortical thickness in certain areas between tp1
and tp2 followed
Hi Martin,
That worked! Thanks a lot,
Seán
On 23 June 2011 18:22, Martin Reuter mreu...@nmr.mgh.harvard.edu wrote:
Hi Sean,
I think the --out... names need to be without the ending (mgh)
so for example --out-avg=long23.thickness-avg
Maybe that'll fix it.
Best, Martin
On Thu,
Dear FreeSurfers,
I am looking for a little help comparing longitudinal data. I have three
timepoints on each patient and have been able to get individual
spc-thickness maps using the long_mris_slopes command where my table
included all three time points. I would however like to compare
Hi Sean,
I think the --out... names need to be without the ending (mgh)
so for example --out-avg=long23.thickness-avg
Maybe that'll fix it.
Best, Martin
On Thu, 2011-06-23 at 09:12 -0700, Seán Froudist Walsh wrote:
Dear FreeSurfers,
I am looking for a little help comparing longitudinal
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