[Freesurfer] qdec problem

Hi,Douglas maybe, you are right. i have tried most of new versions, as follows, but the problem still has. I don't know whether Fedora (3.14-288,fc20.x86_64) 20 (Heisenbug) match with these versions. thank you very much. freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0

Re: [Freesurfer] Multi-band slice timing correction

Hi, One comment: I don’t know about the details of these particular scripts, but users should be aware that different SMS/MB implementations (e.g., CMRR vs. Siemens/MGH) do not necessarily use the same slice ordering. The safest thing to do is confirm the timing from the DICOMs. cheers, -MH

Re: [Freesurfer] Converting RAW data to ANALYZE format

what is raw format? On 09/07/2016 07:03 PM, Maryam Kouchakidivkolaei wrote: > Dear experts: > I have bunch of files in RAW format, how can I convert them to NIFTI or > ANALYZE format? > > Any help would be appreciated. > Thanks, > Maryam > ___ >

[Freesurfer] Converting RAW data to ANALYZE format

Dear experts: I have bunch of files in RAW format, how can I convert them to NIFTI or ANALYZE format? Any help would be appreciated. Thanks, Maryam ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] qdec: Generate Stats Data tables {Disarmed}

Hello, you are right, further up I get an error, that it couldnt find the subjects in the SUBJECTS_DIR So I tried bert, which I copied into my SUBJECTS_DIR, but this doesnt work either.. It should be enough for qdec to find the subjects directory, if the SubjID (in the qdec.table.dat) is

Re: [Freesurfer] Matrix is ill-conditioned (mri_glmfit)

Try demeaning RBCFolate On 09/01/2016 12:27 PM, Rodriguez-Thompson, Anais wrote: > Hi FreeSurfer experts, > > When running mri_glmfit I am getting the error "matrix is ill-conditioned or > badly scaled, condno=10182.4" > > My fsgd file is attached to this email. > > My command is: > >

[Freesurfer] extract JUST pial surface for brain-printing purposes - what can I skip?

Hi Freesurfer list, Say I was interested ONLY in extracting the pial surface for the purpose of getting a 3D print of a brain. Are there any time-intensive steps that can I safely exclude from the recon-all pipeline? For example, if I exclude the CARegister step ( -nocareg ), will I still

Re: [Freesurfer] Qdec Error: Couldn't open qcache file

*Can you send the terminal output for recon-all -s subjid -qcache* On 09/01/2016 02:53 PM, Jana Dinges wrote: > Dear freesurfer community, > we are conducting cortical-thickness analysis using freesurfer-5.3.0 and have > been experiencing some problems with the final analysis steps. > We are

Re: [Freesurfer] Multi-band slice timing correction

On 09/01/2016 04:31 PM, Wang, Ruosi wrote: > Dear Freesurfer developers: > > I'm seeking out ways for performing multi-band slice timing correction > with freesurfer 5.3. I've searched the mailing list, and noticed that > there might be a couple of ways for doing this. But, I still have some

Re: [Freesurfer] qdec problem

Sounds like the GUI is doing strange things. What platform are you running on? What version of FS? Can you try it on a different type of computer? On 09/07/2016 08:20 AM, wanghaibao wrote: > Hi, /Douglas/ > thank you for your reply. > > yes, the number in the text box cannot be changed,

Re: [Freesurfer] qdec: Generate Stats Data tables {Disarmed}

Is that all the terminal output it gave? If not, can you provide the rest? Did it print out an asegstats2table command in the terminal? On 09/07/2016 05:40 PM, c.anastasopou...@lumc.nl wrote: > F5_removeLastScript(document,'F5_cookieInitId');F5_initializeCookiesFromMeta(); > > > Hello, > > I

Re: [Freesurfer] mri_glmfit --pvr Assistance

Try doing a search for pvr on our mail archive http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/ On 09/07/2016 04:12 PM, Timothy Hendrickson wrote: > FreeSurfer Experts, > > I have a data set which comprises one group and the co-variate IQ. I > would like to correlate this data set

[Freesurfer] qdec: Generate Stats Data tables {Disarmed}

Hello, I am facing a problem similar to what others in the community have reported: when trying to "Generate Stats Data tables" in qdec, I get following error: SUBJECTS_DIR is '/home/ubuntubeast/Documents/freesurfer_subj_dir' mkdir -p

Re: [Freesurfer] recon-all error

Hello Yawu, Unfortunately the mni tools shipped with Freesurfer 5.3 are NOT compatible with the version of perl (v5.22) shipped with the latest version of ubuntu (16.04). The easiest solution is to download and install the development version of FreeSurfer from the following page (see

[Freesurfer] mri_glmfit --pvr Assistance

FreeSurfer Experts, I have a data set which comprises one group and the co-variate IQ. I would like to correlate this data set with the dependent measure LGI. I originally performed this in QDEC, however I read elsewhere that a vertex-by-vertex correlation cannot be done in QDEC. Further, I read

Re: [Freesurfer] Extracting aseg.stats data

Is your SUBJETS_DIR set correctly? Probably it should be /home/bmiadmin/Tamara/FreeSurfer_GENFI/analysis/output ie, there needs to be a "/" at the beginning On 09/07/2016 09:48 AM, Tamara Tavares wrote: > Hello, > > I am trying to extract the volumes from the aseg file of multiple > subjects

Re: [Freesurfer] extract thickness values from clusters

I think the way I would do it would be to run mris_preproc for each group and time point to yield a stack of thicknesses for each. Then for each I would run mri_segstats --i lh.stack.group1.tp1.mgh --excludeid 0 --sannot fsaverage lh /path/to/cluster.annot --avgwf

Re: [Freesurfer] design matrix palm

Sorry, I don't know how to use palm either :( On 09/07/2016 04:34 AM, maaike rive wrote: > Hi all, > > I was adviced to use PALM for permutation of non-orthogonal surface > data. However, I have some questions regarding the design matrix en > contrast files to be used in PALM, but somehow I

[Freesurfer] Extracting aseg.stats data

Hello, I am trying to extract the volumes from the aseg file of multiple subjects using the command: asegstats2table --subjects C9F03_1 C9F03_2 C9F07_1 --meas volume --tablefile aseg_stats_test.txt I keep getting the following error: SUBJECTS_DIR :

[Freesurfer] qdec problem

Hi, Douglas thank you for your reply. yes, the number in the text box cannot be changed, including threshold and False Discovery Rate in display. and also when i Save the picture of Display in File menu, the name cannot be input into the text box. Can you not just change the number in the text

[Freesurfer] extract thickness values from clusters

Dear Freesurfer Experts, I did a longitudinal 2 stage model and now I would like to extract the thickness and area values from significant clusters that survived the Monte Carlo correction. As I understood from the various e-mails in the archives expressing the same request there is a file

[Freesurfer] design matrix palm

Hi all, I was adviced to use PALM for permutation of non-orthogonal surface data. However, I have some questions regarding the design matrix en contrast files to be used in PALM, but somehow I cannot subscribe to the FSL mailing list, and I was hoping one of the freesurfer users could help me

[Freesurfer] recon-all error

Dear Freesurfer Developers, After updating my op to Ubunto from 14 to 16.04, and re-installing the Freesurfer, when I run recon-all, it ended with an error message: /media/yw/liu/Liu/freesurfer/subjects/A2090_1/mri mri_nu_correct.mni --n 1 --proto-iters 1000 --distance 50 --no-rescale --i

Re: [Freesurfer] Cluster Forming Threshold

Hi Tim, There is no established criterion and a recent, useful guideline is perhaps use the threshold that would correspond to a p=0.001, that is, about 3.1 in a z-map (see Woo et al., Neuroimage, 2014 ). All the best, Anderson On 1