k you so much!
Clara
--
Clara Kühn, Phd Candidate
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany
Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mai
k you so much!
Clara
--
Clara Kühn, Phd Candidate
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany
Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mai
etreff: Re: [Freesurfer] extract values for significant cluster
You can use mri_segstats specifying the ocn as the segmentation, the
stack of thicknesses as the input, and --avgwf file.dat as the output.
Make sure to add --excludeid 0 to exclude background voxels
On 07/27/2017 06:18 AM, Clara Kühn wro
ones I received in the cache.th30.abs.y.ocn.dat
file)
Could you please tell me if this is possible and how?
Thank you very much!
Clara
--
Clara Kühn, Phd Candidate
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany
and how it can be fixed?
How long is this step supposed to take? I have 81 subjects with 1 - 3 time
points.
Any help or suggestions would be much appreciated!
Cheers
Clara
--
Clara Kühn, Phd Candidate
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Step
tep supposed to take? I have 81 subjects with 1 - 3 time
points.
Any help or suggestions would be much appreciated!
Cheers
Clara
--
Clara Kühn, Phd Candidate
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany
Phone:
ne...
I've also attached the input file.
What could be the problem and how can I fix it?
Cheers Clara
--
Clara Kühn, Phd Student
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany
Phone:
the first subject in the list
works fine...
I've also attached the input file.
What could be the problem and how can I fix it?
Cheers Clara
--
Clara Kühn, Phd Student
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Ger
with the Longitudinal Two Stage Model by looking at the
> spc from tp1 to tp2 and then looking at the spc from tp2 to tp3?
>
> Are there statistical reasons that forbid this procedure of comparing the
> change across time between groups?
>
> Thanks for your help!
> Clara
&g
with the Longitudinal Two Stage Model by looking at the
> spc from tp1 to tp2 and then looking at the spc from tp2 to tp3?
>
> Are there statistical reasons that forbid this procedure of comparing the
> change across time between groups?
>
> Thanks for your help!
> Clara
&g
the spc from tp2 to tp3?
Are there statistical reasons that forbid this procedure of comparing the
change across time between groups?
Thanks for your help!
Clara
--
Clara Kühn, Phd Student
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse
spc from tp2 to tp3?
Are there statistical reasons that forbid this procedure of comparing the
change across time between groups?
Thanks for your help!
Clara
--
Clara Kühn, Phd Student
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
same no of
columns
oh, I think I see the problem now. The input is surface-based data, but
you did not include a --surf subject hemi option, so it thinks that it
is a volume.
On 04/11/2017 12:58 PM, Clara Kühn wrote:
> Hi Doug,
>
> attached you find the rmanova directory after I ran the mr
mns
sorry, that is the log file. What I want is the terminal output, ie, when you
run it, all the stuff that is printed to the screen.
On 4/11/17 5:07 AM, Clara Kühn wrote:
Hi Doug
I am not conciously using a mask but I attached the glmfit.log
At the end it actually states "ResidualFWHM
the terminal
output from running mri_glmfit?
On 03/31/2017 03:29 AM, Clara Kühn wrote:
> ah, ok. I used the proper glmdir now with this command:
> mri_glmfit-sim --glmdir
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2/qdec/rmanova/
> --cache-dir
> /data/p_npsy001_n
03/30/2017 01:12 PM, Clara Kühn wrote:
> I tried this command:
>
> mri_glmfit-sim --glmdir
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//qdec/rmanova/C-pre-vs-post
> --cache-dir
> /data/p_npsy001_neurotrain/kids_data/sem_con-tp1and2//average/mult-comp-cor/
> --cache
"
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Donnerstag, 30. März 2017 18:57:36
Betreff: Re: [Freesurfer] glmfit mismatch between X and C with same no of
columns
what do you mean that it did not seem to work?
On 03/30/2017 11:25 AM, Clara Kühn wrote:
> Thank you! I completely didn't s
re 40 subjects, you would only have 40+1 columns, not 80+1
On 03/29/2017 03:42 AM, Clara Kühn wrote:
> Hi Doug,
>
> I've also attached the fsgd file for you. Yes, I have 40 subjects and a
> contrast column. I adapted this from this tutorial:
> https://surfer.nmr.mgh.harva
sed on DODS and not
DOSS (see the web page on the rmanova about creating contrasts)
On 03/28/2017 03:50 AM, Clara Kühn wrote:
> Sorry, I had a typo in the fsgd file. This is the correct command line and
> terminal output:
>
> mri_glmfit --glmdir $SUBJECTS_DIR/qdec/rmanova/ --y
>
, C has 81 cols
- Ursprüngliche Mail -
Von: "Douglas N Greve"
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Montag, 27. März 2017 19:49:04
Betreff: Re: [Freesurfer] glmfit mismatch between X and C with same no of
columns
Need command line and terminal output
On 03/27/2017 09:08
: "Douglas N Greve"
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Montag, 27. März 2017 19:49:04
Betreff: Re: [Freesurfer] glmfit mismatch between X and C with same no of
columns
Need command line and terminal output
On 03/27/2017 09:08 AM, Clara Kühn wrote:
> Dear Freesurfer experts,
&
ns...
Any help would be much appreciated, thank you!
Clara
--
Clara Kühn, Phd Student
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany
Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mail: ck
the vertices in the ROI, which is
not what you want for surface area. Add --accumulate to the mri_segstats
command line to get the total area
On 02/21/2017 12:43 PM, Clara Kühn wrote:
> I have one last question about the whole thing.
>
> What is the measurement in the output file? My
.mgh.harvard.edu
Gesendet: Dienstag, 21. Februar 2017 18:23:48
Betreff: Re: [Freesurfer] cluster as ROI
then that is the "ocn" file to use with mri_segstats
On 02/21/2017 12:18 PM, Clara Kühn wrote:
> yes!
>
> - Ursprüngliche Mail -
> Von: "Douglas N Greve&q
gstats
On 02/21/2017 12:18 PM, Clara Kühn wrote:
> yes!
>
> - Ursprüngliche Mail -
> Von: "Douglas N Greve"
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Dienstag, 21. Februar 2017 17:58:37
> Betreff: Re: [Freesurfer] cluster as ROI
>
> Does t
_again//rh-Diff-1-3-Intercept-long.area-spc/cache.th30.abs.sig.ocn.mgh
On 02/21/2017 11:54 AM, Clara Kühn wrote:
> I've attached it for you as a .txt file
>
> - Ursprüngliche Mail -
> Von: "Douglas N Greve"
> An: freesurfer@nmr.mgh.harvard.edu
> Ge
I've attached it for you as a .txt file
- Ursprüngliche Mail -
Von: "Douglas N Greve"
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Dienstag, 21. Februar 2017 17:47:23
Betreff: Re: [Freesurfer] cluster as ROI
Can you send the terminal output?
On 02/21/2017 11:44 AM, C
- Ursprüngliche Mail -
Von: "Douglas N Greve"
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Dienstag, 21. Februar 2017 17:24:02
Betreff: Re: [Freesurfer] cluster as ROI
You will have to run mri_glmfit-sim
On 02/21/2017 04:07 AM, Clara Kühn wrote:
> Hi Doug,
>
> I have a gamma
-
Von: "Douglas N Greve"
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Donnerstag, 16. Februar 2017 19:22:01
Betreff: Re: [Freesurfer] cluster as ROI
On 02/16/2017 04:24 AM, Clara Kühn wrote:
> Hi Doug,
>
> thanks for your input. Could you specify some of the flags for me?
>
&g
ri_segstats --i tp1.stack.mgh --seg glmdir/contrast/csdbase.sig.ocn.mgh
--excludeid 0 --avgwf tp1.clustermean.dat
The output tp1.clustermean.dat will be a matrix with nsubjects rows and
nclusters columns where the value represents the mean for that subject
in that cluster.
On 02/14/2017 11:47
didn't work (I
could draw only on the medial surface and around the temporal sulcus). I'm
guessing because I'm using a study specific template and not the fsaverage.
Any help is much appreciated!
Thank you
Clara
--
Clara Kühn, Phd Student
Max-Planck-Institute for Human Cognitive an
.abs.sig.cluster.mgh.stats
is not found or is too small to be a valid statsfile
Use --skip flag to automatically skip bad stats files
Do I have to define my cluster as a ROI and then warp it onto the single time
points? How would I do that?
Any help is much appreciated!
Thank you
Clara
--
Clara Kühn
ns
On 02/08/2017 11:38 AM, Clara Kühn wrote:
> Thank you, I think it worked. I've attached the file again.
> There was one error message in the terminal output though:
>
> atlas_icv (eTIV) = 1287829 mm^3(det: 1.512705 )
> /nobackup/etsch2/kids/prepost-61kids//ZF1K.bas
ath when
running it, like this
$SUBJECTS_DIR/mris_anatomical_stats-doug
On 02/08/2017 11:27 AM, Clara Kühn wrote:
> I'm so sorry, I don't know anything about programming...
> I downloaded it, copied it into my SUBJECTS_DIR as mris_anatomical_stats-doug
> and tried
it with the v5.3 version
On 02/08/2017 10:53 AM, Clara Kühn wrote:
> thanks. What kind of format is it? How do I open it?
>
> Cheers
> Clara
>
> - Ursprüngliche Mail -
> Von: "Douglas N Greve"
> An: freesurfer@nmr.mgh.harvard.edu
> Gesendet: Mit
6)
https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_anatomical_stats
On 02/08/2017 04:55 AM, Clara Kühn wrote:
> Hi Doug,
>
> thanks for your reply. I tried it out and attached the lh.aparc.pial.stats
> file for you to take a look at. As far as I can tell it's still rep
parc.annot.ctab subject lh pial
On 2/7/17 4:48 AM, Clara Kühn wrote:
> Dear FreeSurfer experts,
>
> I'm trying to extract a total Pial Surface Area like it is extracted for
> White Surface Area in the ?h.aparc.stats file. I have tried this command but
> it doesn&
Dear FreeSurfer experts,
I'm trying to extract a total Pial Surface Area like it is extracted for White
Surface Area in the ?h.aparc.stats file. I have tried this command but it
doesn't seem to include Pial Surface Area:
mris_anatomical_stats -a $SUBJECTS_DIR/ZF1K.base/label/lh.aparc.annot -f
the sumfile for the cluster identity
On 02/01/2017 11:41 AM, Clara Kühn wrote:
> Dear FreeSurfer experts,
>
> I did a group analysis in QDEC for the symmetric percent change from pre to
> post and have a couple of clusters that don't survive the Monte Carlo
> correction. I want t
n 150 vertices to look at individual trends.
How could I achieve this?
Thank you for your help.
Clara
-----
Clara Kühn, Phd Student
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany
Phone: +49 341 - 9940 2271
Fax: +4
ou like (e.g. cortex,
superior temporal cortex, etc.)
check the "--label" option of mri_glmfit. see also:
https://surfer.nmr.mgh.harvard.edu/fswiki/BuildYourOwnMonteCarlo
-joost
<http://www.cibersam.es/grupos/grupo-de-investigacion/ficha-personal?id=14486>
On Wed, Jan 11, 2017 at
exactly the effects are.
I'd be really happy for any suggestions!
Thank you
Clara
--
Clara Kühn, Phd Student
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany
Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 226
ike to show that the significant difference between two groups is
driven by a certain group and to do that I want to display the thickness and
area values of each cluster in bar graphs.
What could I do to receive these values?
Cheers, Clara
--
Clara Kühn, Phd Student
Max-Planck-Institute for
Hello Ben,
I am no expert, I can only talk from my experience.
I've had similar images in my data. Those might be blood vessels or dura that
were included in the surface. If they are included in the surface on more than
5 slices and pretty well visible you could delete those voxels from the
br
eers
Clara
- Ursprüngliche Mail -
Von: "Douglas Greve"
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Mittwoch, 31. August 2016 15:57:25
Betreff: Re: [Freesurfer] REPOST: problem with Qdecrc file
Try long_mris_slopes
On 8/31/16 8:34 AM, Clara Kühn wrote:
> Dear FreeSurfer exp
Dear FreeSurfer experts,
I still don't seem to be able to choose spc and rate etc from the dropdown menu
in QDEC. Is there an option to perform the longitudinal 2 stage model in the
command line instead of QDEC?
Thank you!
Clara
- Ursprüngliche Mail -
Von: "ckuehn"
An: "Freesurfer sup
Hi Martin,
I tried both. Neither of the options worked, though.
I have created a subdirectory SUBJECTS_DIR/qdec2stage/ where I have my dat
file, the .Qdecrc, the level files etc. But when I start qdec in that folder,
load the data table and prepare everything I still can't choose spc (for
examp
ght be the
problem?
Thank you for your help!
Clara
--
Clara Kühn, Phd Student
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany
Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mail: cku...@
ght be the
problem?
Thank you for your help!
Clara
--
Clara Kühn, Phd Student
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany
Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mail: cku...@
Thanks for your help!
Clara
--
Clara Kühn, Phd Student
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany
Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mail: cku...@
Juli 2016 23:46:20
Betreff: Re: [Freesurfer] DeMean Flag
The DeMeanFlag in what tool?
On 07/08/2016 05:16 AM, Clara Kühn wrote:
> Dear Freesurfer experts,
>
> is there an explanation somewhere for the DeMeanFlag? I can't find it in the
> wiki but I would like to use it to deme
d you please explain it on the example design matrix so I can adapt it to
mine?
Thank you!
Clara
--
Clara Kühn, Phd Student
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany
Phone: +49 341 - 9940 2271
Fax: +4
Dear Freesurfer experts,
is there an explanation somewhere for the DeMeanFlag? I can't find it in the
wiki but I would like to use it to demean my covariates for the GLM and LME.
Cheers
Clara
--
Clara Kühn, Phd Student
Max-Planck-Institute for Human Cognitive and Brain Science
Departme
ischl"
An: "Freesurfer support list"
Gesendet: Montag, 4. Juli 2016 15:37:57
Betreff: Re: [Freesurfer] controlling for total gray matter volume
sounds right to me
Bruce
On Mon, 4 Jul 2016, Clara Kühn wrote:
> I have decided now to not control for ICV or total gray matter volume when
>
Ok, thanks!
- Ursprüngliche Mail -
Von: "Bruce Fischl"
An: "Freesurfer support list"
Gesendet: Montag, 4. Juli 2016 15:37:57
Betreff: Re: [Freesurfer] controlling for total gray matter volume
sounds right to me
Bruce
On Mon, 4 Jul 2016, Clara Kühn wrote:
> I
I have decided now to not control for ICV or total gray matter volume when
looking at cotrical thickness but to control for total gray matter volume when
looking at surface area. Does that sound about right?
Cheers, Clara
- Ursprüngliche Mail -
Von: "Arkadiy Maksimovskiy"
An: freesurfe
wondering if it is useful to control for total gray matter volume
when looking at surface area?
Thanks for your help!
Clara
--
Clara Kühn, Phd Student
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany
Phone: +49
Dear FreeSurfer experts,
I would like to look at longitudinal thickness data and want to control for
total gray matter volume. Should I use that information from the CROSS before
anything has been registered and smoothed or from the LONG after they have been
registered to the BASE?
Also I was w
variable (in my case whole brain
cortical thickness/surface area)?
Thank you!
Clara
--
Clara Kühn, Phd Student
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany
Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
variable (in my case whole brain
cortical thickness/surface area)?
Thank you!
Clara
--
Clara Kühn, Phd Student
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany
Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web
-out examples?
http://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples
On 05/31/2016 03:39 AM, Clara Kühn wrote:
> Dear FreeSurfer experts,
>
> I would like to correlate my thickness data with behavioral measures. Can I
> do that with glmfit? If so, could you explain how to specify the contrast for
&
Dear FreeSurfer experts,
I would like to correlate my thickness data with behavioral measures. Can I do
that with glmfit? If so, could you explain how to specify the contrast for that?
My fsgd file looks like this:
GroupDescriptorFile 1
Class 1male plus blue
Class 1female plus red
Class 2male
Dear FreeSurfer experts,
I would like to correlate my thickness data with behavioral measures. Can I do
that with glmfit? If so, could you explain how to specify the contrast for that?
My fsgd file looks like this:
GroupDescriptorFile 1
Class 1male plus blue
Class 1female plus red
Class 2male
fer] glmdir question
Try this version
ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/mri_glmfit-sim
On 05/26/2016 12:53 PM, Clara Kühn wrote:
> Hi Doug,
>
> I ran this command with the --no-y Flag:
>
> mri_glmfit-sim --glmdir
> $SUBJECTS_DIR/qdec
bject. The columns are the clusters. Each cell is the mean of the
input for that subject over that cluster. It needs the input data to do
this.
On 05/26/2016 11:18 AM, Clara Kühn wrote:
> I thought it had to be there because when I don't copy it into the glmdir I
> get an error messa
the glmdir). In any
case, you can run it with --no-y and it will not look for the input file
(and will not compute means over the clusters).
On 5/26/16 8:56 AM, Clara Kühn wrote:
> Dear FreeSurfer Experts,
>
> when running the Monte Carlo correction on a GLM I specify this command:
&g
Clara
--
Clara Kühn, Phd Student
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany
Phone: +49 341 - 9940 2271
Fax: +49 341 - 9940 2260
Web: www.cbs.mpg.de
E-Mail: cku...@cbs.m
ecified in the --f or --fsgd options
On 04/14/2016 12:08 PM, Clara Kühn wrote:
> Hi Martin,
>
> thanks for your reply.
>
> I have two further questions on that matter:
>
> 1. I opened the stacked file (lh.thickness_sm10.mgh) in matlab but there is
> no column for subject-id o
stack the
lh.thickness.fwhm10.87kids_template.mgh together into one file you
should get the same thing as the output of mris_preproc. With
mris_preproc, you have to keep track of the order of the subjects as
specified in the --f or --fsgd options
On 04/14/2016 12:08 PM, Clara Kühn wrote:
> Hi Martin,
>
&
Hi Martin,
thanks for your reply.
I have two further questions on that matter:
1. I opened the stacked file (lh.thickness_sm10.mgh) in matlab but there is no
column for subject-id or anything to give me a hint which line is which
subject. Is there a way to find that out? Is it in the same orde
guidelines.
On 4/13/16 8:36 AM, Clara Kühn wrote:
> Hi Doug,
>
> thanks for your reply. It made things a lot clearer. I totally understand
> that you're probably receiving more than one cry for help per day.
>
> What would you say are the conventions for picking a thresh
as 72 rows."
I have looked at mri_glmfit-sim --help but there seems to be no flag for fwhm
only an overwriting one.
Should I register and smooth the data again for the separate time points or is
there another way to deal with that?
What could I do to correct my glm data?
Cheers, Clara
--
Clar
Mail -
Von: "Douglas N Greve"
An: freesurfer@nmr.mgh.harvard.edu
Gesendet: Mittwoch, 13. April 2016 00:15:41
Betreff: Re: [Freesurfer] REPOST: Monte Carlo correction in QDEC
sorry, I could have sworn that I answered this one
On 04/12/2016 08:57 AM, Clara Kühn wrote:
> Dear FreeSurfe
Dear FreeSurfer experts,
for the analysis in QDEC I created my own Monte Carlo correction.
My questions relate to the threshold option.
1. Would I use neg if I have mostly blue clusters in the QDEC display and pos
if I have mostly red clusters?
2. When do I use abs?
3. I compared the neg opti
Dear FreeSurfer experts,
for the analysis in QDEC I created my own Monte Carlo correction.
My questions relate to the threshold option.
1. Would I use neg if I have mostly blue clusters in the QDEC display and pos
if I have mostly red clusters?
2. When do I use abs?
3. I compared the neg optio
and Qdec can only do 2 levels. Qdec is
rather limited. You need to use mri_glmfit for that.
Best, Martin
On 04/08/2016 08:14 AM, Clara Kühn wrote:
> Dear FreeSurfer experts,
>
> I am trying to analyze some single time points of my longitudinal data in
> QDEC. I have 3 groups and cre
Dear FreeSurfer experts,
I am trying to analyze some single time points of my longitudinal data in QDEC.
I have 3 groups and created a file for the discrete factor "group" with three
levels (1,2 and 3). I have done the same for gender (with 2 levels). The
analysis with gender works just fine b
Dear FreeSurfer experts,
I am trying to analyze some single time points of my longitudinal data in QDEC.
I have 3 groups and created a file for the discrete factor "group" with three
levels (1,2 and 3). I have done the same for gender (with 2 levels). The
analysis with gender works just fine b
Dear FreeSurfer experts,
I am trying to analyze some single time points of my longitudinal data in QDEC.
I have 3 groups and created a file for the discrete factor "group" with three
levels (1,2 and 3). I have done the same for gender (with 2 levels). The
analysis with gender works just fine bu
moothing. It can
compute rate (slope of linear fit) or some percent change measures, also
the average across time.
mris_preproc is a tool to stack and map data to the global template
(fsaverage) and apply smoothing etc. It does not perform any fitting.
Best, Martin
On 03/24/2016 12:44 PM, Clar
ailable later. You can do that even on the
long runs, or you can just manually map ans smooth things with preproc.
6) A different preproc call using a fsgd file rather than a qdec table.
see the glm_fit tutorial for these things.
Best, Martin
On 03/23/2016 12:28 PM, Clara Kühn wrote:
> Dear Fre
dec/cross.qdec.table.dat
(5) recon-all -s name -qcache -target name_of_template
(6) mris_preproc --fsgd gender_age.fsgd --cache-in thickness.fwhm10.fsaverage
--target fsaverage --hemi lh --out lh.gender_age.thickness.10.mgh
Please help clear up my confusion :)
Thanks in advance,
Clara
--
Clara Kühn, Phd Stud
Hi Kaspar,
I had the same problem. The last version that supports matlabpool is Matlab
8.2. Maybe try it with that version.
Cheers, Clara
- Ursprüngliche Mail -
Von: "Kasper Jessen"
An: "Freesurfer support list"
Gesendet: Mittwoch, 23. März 2016 09:41:51
Betreff: [Freesurfer] Matlabpo
mi lh --meas thickness
--out lh.thickness.mgh?
The possibilities and the ever so slightly changing commands are somewhat
overwhelming, sorry...
Thanks in advance,
Clara
--
Clara Kühn, Phd Student
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanst
different directory, then use the --cache-dir
option when running mri_glmfit-sim to specify the new folder, eg, if you
use --o /path/to/myspace/yoursubject/lh/cortex, then specify
/path/to/myspace
On 03/15/2016 12:36 PM, Clara Kühn wrote:
> Dear FreeSurfer experts,
>
> I have a que
Dear FreeSurfer experts,
I have a question regarding the Monte Carlo correction.
To create a Monte Carlo correction for my specific sample (4year old kids) the
wiki suggests this command:
mri_mcsim --o $FREESURFER_HOME/average/mult-comp-cor/yoursubject/lh/cortex
--base mc-z --surface yoursubject
Dear FreeSurfer experts,
I hava a question regarding rerunning the recon-process. I have cases where I
do manual edits on a brain and only set a few control points on one hemisphere
but white matter edits on the other. I would then run the -cp flag for one
hemisphere and the -wm flag for the o
Dear FreeSurfer experts,
I hava a question regarding rerunning the recon-process. I have cases where I
do manual edits on a brain and only set a few control points on one hemisphere
but white matter edits on the other. I would then run the -cp flag for one
hemisphere and the -wm flag for the ot
you are getting an error with the other hemisphere.
Maybe you use a different template for qcache and then fsaverage later?
Best, Martin
On 12/11/2015 11:36 AM, Clara Kühn wrote:
> Hi Freesurfer experts,
>
> I eventually used the recon-all -s subjectname -qcache -target my_template t
ubject and then use qdec.
If you want to make use of the improved data from the longitudinal image
processing, you need to specify the *.long.base directories, so that
data is taken from there.
Good luck, Martin
On 12/08/2015 04:24 AM, Clara Kühn wrote:
> Dear FreeSurfer experts,
>
>
e with the first row fsid
timepoint1.long.base
for each subject and then use qdec.
If you want to make use of the improved data from the longitudinal image
processing, you need to specify the *.long.base directories, so that
data is taken from there.
Good luck, Martin
On 12/08/2015 04:24 AM, Clar
from the Base, right?
So, I would like to know how I can analyzse a single time point within my
longitudinal design.
Cheers,
Clara
--
Clara Kühn, Phd Student
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany
Phone
to obtain
said volumetric data. Is there an extra turorial or walkthrough for that?
Cheers, Clara
--
Clara Kühn, Phd Student
Max-Planck-Institute for Human Cognitive and Brain Science
Department of Neuropsychology
Stephanstrasse 1A
04103 Leipzig, Germany
Phone: +49 341 - 9940 2271
Fax: +
quot;
Gesendet: Dienstag, 3. November 2015 18:03:52
Betreff: Re: [Freesurfer] Freesurfer crash upon wm.mgz changes
Try 6.0.0beta.
On 11/03/2015 12:02 PM, Clara Kühn wrote:
> Our IT guy said it could be a software problem since he didn't have the
> problem and the only difference betw
eta.
On 11/03/2015 12:02 PM, Clara Kühn wrote:
> Our IT guy said it could be a software problem since he didn't have the
> problem and the only difference between out computers was the display.
> We have these versions at the institute:
>
> 4.0.5 ; 4.1.0 ; 4.5.0 ; 5.0.0 ; 5.1
ara,
can you try the dev version of freeview?
Ruopeng
On 11/03/2015 11:50 AM, Bruce Fischl wrote:
Hi Clara
that doesn't crash for me. Are you sure you ahve write permission to the file?
And that the disk isn't full? Ruopeng: any other ideas?
Bruce
On Tue, 3 Nov 2015, Clara Küh
t means by Segmentation Violation and how I can fix it??
Cheers and thanks in advance!
Clara Kühn
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The information in this e-mail is int
nnerstag, 13. August 2015 22:10:26
Betreff: Re: [Freesurfer] cannot find qdec file
I'm not sure what to tell you. When I use the new file I don't get an
error. When I use the old one I do. Can you run
mris_preproc --debug --qdec-long long.qdec.table.dat
and send me the result?
On 08/13/20
e
Can you send the new qdec table file?
On 08/05/2015 04:05 AM, Clara Kühn wrote:
> no worries!
> sadly, though, deleting the empty line wasn't the answer to the problem :(
> Cheers, Clara
>
> - Ursprüngliche Mail -
> Von: "Douglas N Greve"
> An: fre
le
oops, sorry for the delay, thanks for the reminder. The problem is that
you have a blank line at the end of your long.qdec.table.dat file.
Remove the line and see if it works.
doug
On 08/04/2015 12:42 PM, Clara Kühn wrote:
> Hi Doug,
> did the fordoug.log file give any information about
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