Re: [Freesurfer] selxavg3 problems - missing mcextreg files

Hi Adam, mcextreg files are generated by preproc-sess. If you don't have these files in your bold/015/ folder than preproc-sess might not have been completed. Pratap > Hi all, > > I'm having an issue with selxavg3-sess in Stable 4. I've run all commands > up to this point without error. Here wa

Re: [Freesurfer] restricting mri_glmfit to cortical regions

Hi Prapti, A work around can be try running mri_glmfit with --label yourRoilabel flag, and then run mri_glmfit-sim. mri_glmfit --y ... --fsgd --surf --C --glmdir --label mri_glmfit-sim --sim .. --glmdir -

Re: [Freesurfer] manually continue surfcluster on unfinished sim?

Hi Victoria, Regarding mri_surfcluster, You can still use mri_surfcluster with --in --csd --sum --cwsig flags. more info, mri_surfcluster --help thanks pratap > Hi, > > I am processing several multiple comparison jobs on launchpad: > > 'mri_glmfit-sim --glmdir > lh.physio2_chol_final.cvram.115

Re: [Freesurfer] Re: 'Max' in sig.cluster.summary

Hi Judith, Yes thickness. The MAX indicates the maximum -log10(pvalue) in that cluster. > Hi all. After looking over our monte-carlo results, I a simple question > about the sig.cluster.summary output. > > Is the " Max" in column 2 below a measurement of thickness? > thickness, is the correct int

Re: [Freesurfer] cluster correction - time to finish?

Hi Natham, This should not take that long. For me, it has never been more than 2-3 days for 5000 interactions using mc-z. > Hi all, > > I have started working with clusterwise correction, and initially > attempted to run the mri_glmfit mc-z script with 6000 iterations. After > two weeks it stil

Re: [Freesurfer] clusterwise multiple comparison correction

Libby, Use mri_glmfit-sim instead of mri_glmfit. https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis If you use just mri_glmfit then you have to use mris_surfcluster to get CWP information from .csd file. pratap > hello, > > i am working through the group analysis and multiple co

Re: [Freesurfer] avg ROI

Hi Gabriel, You can do that by using mri_lablel2label and mri_anatomical_stats pratap > > I have created a ROI in an average subject, how can i transpose that ROI > to each subject? > > i mean, use it like a mask to make some statistics on each subject > > > > Regards > > Gabriel > > > > > >

Re: [Freesurfer] permutation / mc-z simulation failure?

Hi Rysia, Your commands looks fine to me, and 5000 iterations is good enough to see significant cluster. You might want to try lowering your threshold to 1.3 (0.05 p value). thanks pratap > Hello, > > > > I have just run a number of permutation and mc-z on data that was > previously analysed us

Re: [Freesurfer] getting vertex numbers

Hi, Try like this, Click inside your blobs. Then click on the Custom Fill botton and then select "upto functional value below threshold". This will select the cluster above the given p value (1.3 in our case). Then click "fill". Then click file->label->save selected label this should work. pr

Re: [Freesurfer] Qdec question

hi Dev, You might have wrong SUBJECTS_DIR, check it using echo $SUBJECTS_DIR > Hi, > I have been running into an error while using Qdec. > *Error in Analyze: Couldn't open file > <$SUBJECT_DIR>//surf/lh.thickness.fwhm10.fsaverage.mgh* > > I checked and the file is there in that folder. I know t

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

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

Re: [Freesurfer] difficulty readings DICOM files from CD

Hi Sam, you can try like this below, umount cdrecorder cd dicom;ls cd ##; ls output will be 2 strings of numbers unpacksdcmdir –src /mnt/cdrom/dicom/INITIAL#/1STof2#’s -targ ./ –scanonly unpacklog Repeat command line with second number Make a cfg.file Save as cfg.file in SUBJECT’s folder

Re: [Freesurfer] Error while registering functionals to anatomicals

Hi Krishna, this link should help http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastLinkAnatData > Hi, > > I am getting an error if I try to register my functionals to anatomical > image > (using spmregister-sess command). It is looking for file > 'subjectname'. Here are the steps I did before comi

Re: [Freesurfer] mri_surfcluster problem?

Kara and Lauren, I think Doug has fixed this problem. i had similar problem but it is working now. pratap > Hi Lauren (and Doug), >> I'm having the same issue. I ran montecarlo simulations on Friday and >> then >> tried to use the results in mri_surfcluster. It ran, but I also got the >> same

Re: [Freesurfer] Focusing on Relevant Areas

Hi MOe, You can make a label file of the region of interest from aseg file. One easy way to do using matlab, m = MRIread('aseg.mgz'); m.vol = (m.vol == ## | m.vol == ##); MRIwrite(m,'roi.mgz'); ## get from FreeSurferColorLUT.txt in freesurfer home. pratap > Hello, > > I'm doing a volume analys

Re: [Freesurfer] tksurfer: Load GDF command line?]

HI Tori, I don't think fsgd option is available on the tksurfer or tkmedit command line. It would have nice to load fsgd file on command line instead of loading from tksurfer gui. > Hi All, > I was wondering if there was a flag or command in tksurfer that would > allow me to load a group de

Re: [Freesurfer] question mri_glmfit

Hi, You have a continuous variable "age" in your fsgd file. As far as i know, permutation can't have continuous variables. Try mc-z that should work. pratap > Hi, > > using version 4.0.5 > > i ran the command: > mri_glmfit --y qdec/N83_only_boys.mgh --fsgd qdec/qdec.fsgd doss --surf > fsaverag

Re: [Freesurfer] mri_preproc

Hi Cibu, can you provide more informations using bugr command? also log file? > Hello > When I run the mri_preproc command I am getting the message > ERROR: cannot find fsaverage in /space/barlab_002/users/cibu/dep_LGI > But the fsaverage folder is in the path and subjects_dir is set > correctly

Re: [Freesurfer] mri_glmfit full Monte Carlo simulation run time on tutorial data

Silviu, MC-full is really slow. you can get almost same results using mc-z that is quicker. thanks pratap > Hello! > > I was running the full Monte Carlo simulation on the 40 subjects tutorial > data (following the Group Analysis tutorial, with mri_glmfit from command > line) and I see the sim

Re: [Freesurfer] preproc-sess : Problem with spatial smoothing and brain masking

Hi, can you post the command you used and the log file? > HI, > I ran the preproc-sess command, but in the output for spatial smoothing, > the > fmcsm5 file is not created. It says > > [balaji-goparajus-computer:~/Desktop/subjectdata] balajigo% > spatialsmooth-sess -i fmc -o fmcsm5 -fwhm 5 -fsd b

Re: [Freesurfer] Monte Carlo Simulation w/ custom design matrix

Jerry, can you post your command lines and log file? there should be fwhm.dat along with the y.fsgd. > How did I miss that??? > Thanks! > - Jerry > > On Thu, Apr 17, 2008 at 3:01 PM, Doug Greve <[EMAIL PROTECTED]> > wrote: > >> there should be a fwhm.dat file in the output. >> >> doug >> >> >> J

Re: [Freesurfer] spmregister-sess vs. autoreg-sess

Hi Tren, I've been using spmregister-sess. As you note autoreg-sess and spmregister-sess compute the same matrix but in different ways. autoreg-sess works in two stages. First, it aligns the same-session anatomical to the FreeSurfer anatomical. Next, it computes the registration from the functio

Re: [Freesurfer] Cluster thresholding

different dataset, again just a >>>>>>>>>> simple 2 group >>>>>>>>>> comaprison with no covariates. >>>>>>>>>> >>>>>>>>>> Running this in qdec, and visualizing with a low threshold >&

[Freesurfer] Qdec parcelation display

Hi Nick, Regarding the parcellation display in Qdec; Is it possible to load aparc.a2005.annot instead of aparc.annot? "Parcellation Display: The cortical parcellation is loaded into Qdec upon opening. On the Display tab you can adjust the annotation opacity. " thanks pratap ___

Re: [Freesurfer] selxavg3 issue

Hi Corey, I just ran selxav3, Check my log and output dir (both dof and mask.nii are created), it looks fine. pratap [galen:bold] (nmr-std-env) cd VvI_MK_Analysis/ [galen:VvI_MK_Analysis] (nmr-std-env) LS acfsegLUT.txt allvfix doffsnr.nii fwhm.sum h.nii mask.nii omnibu

[Freesurfer] Brodman areas using tksurfer/tkmedit

Hi, Can tksurfer/tkmedit have Brodman arreas as well as talairach coordinates displayed? thanks pratap ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

[Freesurfer] QA tools--Permission denied??

hi all I tried to use QA tools on the wiki (writen by jpacheco) at https://surfer.nmr.mgh.harvard.edu/fswiki/QATools?action=highlight&value=qa+tools. I got the following error saying permission denied. I could not even copy the QATOOLS to my folder. thanks pratap [galen:S4_HR_LR18_recon] (nmr-s

Re: [Freesurfer] Re: Error: Cannot allocate memory

I am also getting the same error as below. > Hi Chris, > > Can you forward me to the person I could ask about this issue? > > I've been running jobs the same way using freesurfer for months and today > I keep gettting this error message: Cannot allocate memory > > i.e. > mri_convert orig.mgz ./tm

Re: [Freesurfer] mri_volcluster --ERROR: you must specify a pos or neg sign with --fwhm]

Nevermind, it works fine now with after i added "--sign < >" flag to the mri_volcluster ..command. thanks pratap Original Message Subject: [Freesurfer] mri_volcluster --ERROR: you must specify a pos or neg sign with --fwhm From:[EMAIL

[Freesurfer] ERROR: mri_convert --child killed: segmentation violation

". i will appreaciate for help Pratap Kunwar unpacking config -- {1 scout DICOM blah} {33danat COR blah} {4 3danat COR blah} {5fm_dti DICOM blah} {6fm_dti DICOM blah} {7dti DICOM blah} {14 t2conv bsh

[Freesurfer] spatialsmooth-sess help!

Dear All, I am a new user of FreeSurfer. I am getting the following error when i run spatialsmooth-sess command. ERROR: cannot find /usr/local/freesurfer/stable4/fsl/bin/ip ERROR: ipfsl failed Also, I could not find ip in the bin folder. Will appreciate for help sincerely, pratap __