[Freesurfer] what order for longitudinal edits

process partially (eg. with the -wm flag) and when it is necessary to go back to the base... I am very thankful for any kind of revelation on these matters :) Cheers, Clara Kühn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] what order for longitudinal edits

if that is approximately true, it could work (e.g. short time intervals). Otherwise you may run into lot's of editing problems and it may be easier to just use the cross sectionals in your analysis (at the cost of increased measurement variability). On 05/28/2015 10:19 AM, Clara Kühn wrote: Dear

Re: [Freesurfer] too much white matter

in the interior of the WM? If you want to upload the subject we will take a look cheers Bruce On Mon, 29 Jun 2015, Clara Kühn wrote: Dear Freesurfer experts, I've had this problem now a couple of times: after setting a few (in this case 2) control points and rerunning the recon-all process

Re: [Freesurfer] too much white matter

to upload the subject we will take a look cheers Bruce On Mon, 29 Jun 2015, Clara Kühn wrote: Dear Freesurfer experts, I've had this problem now a couple of times: after setting a few (in this case 2) control points and rerunning the recon-all process with the -cp flag I get huge areas

Re: [Freesurfer] cannot find qdec file

find qdec file can you run mris_preproc --debug --qdec-long /scr/etsch2/kids/ct/qdec/long.qdec.table.dat --target 7kids_template_sc1 --hemi lh --meas thickness --out /scr/etsch2/kids/ct/qdec/lh.thickness.mgh | tee fordoug.log and send me fordoug.log ? On 8/3/15 10:38 AM, Clara Kühn wrote

Re: [Freesurfer] cannot find qdec file

: [Freesurfer] cannot find qdec file you have to give it the entire path to the file On 8/3/15 10:14 AM, Clara Kühn wrote: Dear FS-experts, I want to analyze my longitudinal data with your suggested LME models and am therefore following the walkthrough by J. Bernal. I get an error though very

Re: [Freesurfer] cannot find qdec file

, then it is not the full path. Maybe you need a forward slash (ie, /) in the beginning? On 8/3/15 10:18 AM, Clara Kühn wrote: then I get the error ERROR: cannot find scr/etsch2/kids/ct/qdec/long.qdec.table.dat I had tried that. Sorry, no luck with that. - Ursprüngliche Mail - Von: Douglas Greve gr

Re: [Freesurfer] cannot find qdec file

output, and your long.qdec.table.dat file? On 8/3/15 10:31 AM, Clara Kühn wrote: ok, it can only access the file if I type ls /scr/etsch2/kids/ct/qdec/long.qdec.table.dat (so with the forward slash) but if I then use that path for the mris_preproc command I get nsubjects = 22 ERROR: cannot find

Re: [Freesurfer] too much white matter

? There appears to be very little space between skull and brain so the stripping may be challenging, particularly in the orbitofrontal region where you had this control point (it looks like fat is shifting upwards either into or adjacent to brain) cheers Bruce On Tue, 30 Jun 2015, Clara Kühn

Re: [Freesurfer] too much white matter

will take a look cheers Bruce On Mon, 29 Jun 2015, Clara Kühn wrote: Dear Freesurfer experts, I've had this problem now a couple of times: after setting a few (in this case 2) control points and rerunning the recon-all process with the -cp flag I get huge areas of white matter including

Re: [Freesurfer] cannot find qdec file

qdec file 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

[Freesurfer] cannot find qdec file

Dear FS-experts, I want to analyze my longitudinal data with your suggested LME models and am therefore following the walkthrough by J. Bernal. I get an error though very early on when using the command mris_preproc --qdec-long qdec/long.qdec.table.dat --target 7kids_template_sc1 --hemi lh

Re: [Freesurfer] cannot find qdec file

? On 8/3/15 10:38 AM, Clara Kühn wrote: the command line is this: mris_preproc --qdec-long /scr/etsch2/kids/ct/qdec/long.qdec.table.dat --target 7kids_template_sc1 --hemi lh --meas thickness --out /scr/etsch2/kids/ct/qdec/lh.thickness.mgh the terminal output is this: nsubjects = 22 ERROR: cannot

Re: [Freesurfer] cannot find qdec file

qdec file 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 gr...@nmr.mgh.harvard.edu An: freesurfer

Re: [Freesurfer] cannot find qdec file

--qdec-long long.qdec.table.dat and send me the result? On 08/13/2015 01:01 PM, Clara Kühn wrote: do you mean the one without the blank line at the end? I've attached that for you. Cheers, Clara - Ursprüngliche Mail - Von: Douglas N Greve gr...@nmr.mgh.harvard.edu An: freesurfer

Re: [Freesurfer] Freesurfer crash upon wm.mgz changes

uopeng: any other ideas? Bruce On Tue, 3 Nov 2015, Clara Kühn wrote: Hi Bruce, I attached the wm.mgz from one of my participants. It happens with any participant though. What I did is add wm voxels ( 147, 106, 68 ) and klick the save button and then it crashes with afore mentione

Re: [Freesurfer] Freesurfer crash upon wm.mgz changes

eff: 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 between out computers was the display. > We have these versions at

Re: [Freesurfer] Freesurfer crash upon wm.mgz changes

; <rpw...@nmr.mgh.harvard.edu> An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> 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 gu

[Freesurfer] Freesurfer crash upon wm.mgz changes

by Segmentation Violation and how I can fix it?? Cheers and thanks in advance! Clara Kühn ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mail is intended only

[Freesurfer] correlations with longitudinal data

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: +49

Re: [Freesurfer] correlations with longitudinal data

12/08/2015 04:24 AM, Clara Kühn wrote: > Dear FreeSurfer experts, > > I have a subsample of my longitudinal data with 3 scans per subjects fully > preprocessed and would like to start with some simple correlations of > thickness at time 1 with behavioral measures and other facto

[Freesurfer] obtain volumetric data with qdec

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: +49 341 - 9940 2260 Web: w

Re: [Freesurfer] correlations with longitudinal data

d for example create a qdec table 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

Re: [Freesurfer] correlations with longitudinal data

con-all -long-qcache -target I don't know why 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

[Freesurfer] controlling for ICV in LME

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

[Freesurfer] correlation with glm

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

Re: [Freesurfer] glmdir question

eates 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

Re: [Freesurfer] glmdir question

table. The rows of the table are each subject. 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 glmdi

Re: [Freesurfer] glmdir question

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

Re: [Freesurfer] glmdir question

8:39 Betreff: Re: [Freesurfer] 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 --glmd

Re: [Freesurfer] correlation with glm

n our worked-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

[Freesurfer] glmdir question

-- 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.mpg.de

[Freesurfer] REPOST: controlling for ICV in LME

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

[Freesurfer] REPOST recon-all per hemisphere

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

[Freesurfer] recon-all per hemisphere

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

[Freesurfer] adapt Monte Carlo correction for specific sample

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

Re: [Freesurfer] adapt Monte Carlo correction for specific sample

sample You can just store it in a 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

Re: [Freesurfer] REPOST: Monte Carlo correction in QDEC

- Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> 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 Kü

[Freesurfer] correcting mri_glmfit results

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 -- Clara Küh

[Freesurfer] REPOST: QDEC analysis

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

Re: [Freesurfer] REPOST: QDEC analysis

REPOST: QDEC analysis Hi Clara, I think the message is correct 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 poi

[Freesurfer] Monte Carlo correction in QDEC

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

[Freesurfer] REPOST: Monte Carlo correction in QDEC

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

Re: [Freesurfer] Matlabpool has been removed

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,

Re: [Freesurfer] REPOST: registering longitudinal data to template

, Martin On 03/23/2016 12:28 PM, Clara Kühn wrote: > Dear FreeSurfer experts, > > I would like to analyze my longitudinal data also cross-sectionally at single > time points. I am a little confused as to how to register my data to the > template and smooth it accordingly. > >

[Freesurfer] REPOST: registering longitudinal data to template

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

[Freesurfer] Fwd: QDEC analysis

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

Re: [Freesurfer] REPOST: registering longitudinal data to template

s not perform any fitting. Best, Martin On 03/24/2016 12:44 PM, Clara Kühn wrote: > Thank you, Martin! That clears things up a lot! > > Could you explain what the difference is between the commands > long_mris_slopes and mris_preproc? As far as I understand they give you a > di

[Freesurfer] QDEC analysis

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

Re: [Freesurfer] REPOST: Monte Carlo correction in QDEC

han that, there are not good 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 co

Re: [Freesurfer] correcting mri_glmfit results

me thing. If you 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

Re: [Freesurfer] correcting mri_glmfit results

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

Re: [Freesurfer] correcting mri_glmfit results

ack 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, > > 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

[Freesurfer] LME for surface area

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...@cbs.mpg.de

Re: [Freesurfer] DeMean Flag

ard.edu Gesendet: Montag, 18. 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

[Freesurfer] REPOST: problem with Qdecrc file

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...@cbs.mpg.de

[Freesurfer] LME contrasts

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: +49 341

[Freesurfer] DeMean Flag

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 Department

Re: [Freesurfer] controlling for total gray matter volume

unds 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 > looking at cotrical thickness but to control for total gray matter volume > when looking at surface area. Does that sound about right? >

Re: [Freesurfer] controlling for total gray matter volume

quot; <fis...@nmr.mgh.harvard.edu> An: "Freesurfer support list" <freesurfer@nmr.mgh.harvard.edu> 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

Re: [Freesurfer] controlling for total gray matter volume

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"

[Freesurfer] problem with Qdecrc file

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...@cbs.mpg.de

[Freesurfer] controlling for total gray matter volume

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

[Freesurfer] cotrolling for total gray matter volume

was 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

Re: [Freesurfer] REPOST: problem with Qdecrc file

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

[Freesurfer] extract area.pial stats

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

Re: [Freesurfer] extract area.pial stats

Try this version (same as version 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

Re: [Freesurfer] extract area.pial stats

u don't confuse 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" <gr...@nmr.mgh.harvard.edu> > An: freesur

Re: [Freesurfer] extract area.pial stats

u need to supply the full path 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 tri

Re: [Freesurfer] extract area.pial stats

is expecting v6 naming conventions 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/kid

[Freesurfer] extract values uncorrected clusters

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: +49 341

Re: [Freesurfer] extract area.pial stats

h.aparc.annot -c ../label/aparc.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

Re: [Freesurfer] extract values uncorrected clusters

clusters. Look in 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 >

Re: [Freesurfer] cluster as ROI

- Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> 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

Re: [Freesurfer] cluster as ROI

On 02/21/2017 11:44 AM, Clara Kühn wrote: > Hm. I already did that. In none of my glmdirs are files like the > csdbase.sig.ocn.mgh. This is the mri_glmfit-sim that I ran: > > mri_glmfir-sim --glmdir $SUBJECTS_DIR/qdec/40kids-rh-area-spc --cache-dir > $SUBJECTS_DIR/average/multi-

Re: [Freesurfer] cluster as ROI

016.12.08-40kids-2stagemodel/rh-area_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" <gr...@nmr.mgh.harvard.

Re: [Freesurfer] cluster as ROI

quot;ocn" file to use with mri_segstats On 02/21/2017 12:18 PM, Clara Kühn wrote: > yes! > > - Ursprüngliche Mail - > Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> > An: freesurfer@nmr.mgh.harvard.edu > Gesendet: Dienstag, 21. Februar 2017 17:58:37 > Be

Re: [Freesurfer] cluster as ROI

- Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> An: freesurfer@nmr.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 K

Re: [Freesurfer] cluster as ROI

l be the average value over 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 measureme

Re: [Freesurfer] cluster as ROI

- Ursprüngliche Mail - Von: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> 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: >

[Freesurfer] cluster as ROI

.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

Re: [Freesurfer] cluster as ROI

ter. On 02/14/2017 11:47 AM, Clara Kühn wrote: > Dear FreeSurfer Experts, > > I compared 2 groups in QDEC in spc (from pre to post) and found a cluster > that survives Monte Carlo correction. Now I would like to extract the data > for each participant and each time point from

[Freesurfer] REPOST: longitudinal QDEC cluster as ROI

but that 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 and Brain Science

Re: [Freesurfer] white matter errors due to inhomogeneities (bright spots) in cortex

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

[Freesurfer] extract thickness values from clusters

I would like 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

Re: [Freesurfer] REPOST: problem with Qdecrc file

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"

Re: [Freesurfer] REPOST: problem with Qdecrc file

- Ursprüngliche Mail - Von: "Douglas Greve" <gr...@nmr.mgh.harvard.edu> 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: &

Re: [Freesurfer] vertex-wise ROI analysis

w.cibersam.es/grupos/grupo-de-investigacion/ficha-personal?id=14486> On Wed, Jan 11, 2017 at 2:51 PM, Clara Kühn <cku...@cbs.mpg.de> wrote: > Dear FreeSurfer experts, > > is it possible to do a vertex-wise analysis on ROIs? When I extract the > values per subject for (e.g.)

[Freesurfer] vertex-wise ROI analysis

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 2260 Web

Re: [Freesurfer] glmfit mismatch between X and C with same no of columns

terminal output On 03/27/2017 09:08 AM, Clara Kühn wrote: > Dear Freesurfer experts, > > I'm trying to run a repeated measures anova as described here: > https://surfer.nmr.mgh.harvard.edu/fswiki/RepeatedMeasuresAnova > > I have 40 subjects with 2 time points each, so it's qu

Re: [Freesurfer] glmfit mismatch between X and C with same no of columns

: "Douglas N Greve" <gr...@nmr.mgh.harvard.edu> 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 Kü

Re: [Freesurfer] glmfit mismatch between X and C with same no of columns

columns Since there are 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://su

Re: [Freesurfer] glmfit mismatch between X and C with same no of columns

" <gr...@nmr.mgh.harvard.edu> 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: > Than

Re: [Freesurfer] glmfit mismatch between X and C with same no of columns

ast matrix based 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/r

[Freesurfer] glmfit mismatch between X and C with same no of columns

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: cku...@cbs.mpg.de

Re: [Freesurfer] glmfit mismatch between X and C with same no of columns

between X and C with same no of columns 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

Re: [Freesurfer] glmfit mismatch between X and C with same no of columns

d2//qdec/rmanova On 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-

Re: [Freesurfer] glmfit mismatch between X and C with same no of columns

smatch between X and C with 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 rman

Re: [Freesurfer] glmfit mismatch between X and C with same no of columns

you using a mask? Can you send 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/ > --c

[Freesurfer] REPOST: Two stage model question

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 -- Clara Kühn, Phd Student Max-Planck-Institute for Human Cognitive and Brain Science Department of Neuropsychology Stephanstrasse

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