Re: [Freesurfer] Installing and enabling cuda

Dear Richard, Ok. I will try cuda 8.0 and let you know the result. Should I install cuda 5 before installing cuda 8? or Can I run both? Thanks Ramesh On Tue, May 23, 2017 at 1:54 AM, R Edgar wrote: > On 22 May 2017 at 08:44, Ramesh Babu

Re: [Freesurfer] cuda-gpu problem

Dear Richard, Yesterday I performed single subject analysis with -use-gpu flag and allowed to take its own time to complete. It's get completed within 5.8 hrs. Yes you are correct. I should not interrupt before a final output. And I have realized that gpu and cpu outputs on the terminal are not

[Freesurfer] generating an annotation using Nibabel - how to create last column for ctab?

Dear Freesurfer experts, I'm having trouble generating an annotation file for a large number of ROIs (3000) from Python using Nibabel. The function call that I used is: nib.freesurfer.io.write_annot(filepath, labels, ctab, names) where filepath = 'myFile.annot' labels = numpy 1D array of type

Re: [Freesurfer] Installing and enabling cuda

On 22 May 2017 at 08:44, Ramesh Babu wrote: > After compiling in the same way as given in the webpage, I couldn't reboot. > It was showing a message that "running low graphic mode". It was not opening > the desktop. Then through ctrl+alt+f1, I uninstalled nvida and

Re: [Freesurfer] cuda-gpu problem

On 22 May 2017 at 07:39, Ramesh Babu wrote: > The following last line get repeated same way except (%) in the second line > pasted below. On the third line "Did not call MRIsetResolution", is it error > or normal process? Since repeated many times I thought there is

Re: [Freesurfer] Hyperintensities Volume ?

Hi, Not that I'm aware of. You could use the WM Hypointensities label from aseg though. Despite its understimation of WMH, we have actually found a high correlation with WMH segmented from FLAIRS in over 100 elderly and demented subjects (r < 0.8). Cheers, Elijah Dr. Elijah Mak, Research

[Freesurfer] Hyperintensities Volume ?

Dear FreeSurfer experts: Does the white matter volume shown in the aseg.stats include the hyperintensities volume ? Thanks Best Regards, Yiyu ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Freesurfer white matter outer edge to volume

I don't know about mri_morphology, but you can use mri_binarize to erode. It has several options to allow control of how the erosion is done On 05/22/2017 12:48 PM, Gamaliz wrote: > Douglas, > > I just realized that I was using the wrong feeesurfer output. I had 3 > processed MRIs for the

Re: [Freesurfer] estimated Total Intracranial Volume

I suppose it could, but I don't know why you would. One would really not expect those measures change with head size. If you want to do it, you can fscalc diffusion.nii.gz div eTIV -o diff.scaled.nii.gz where eTIV is th eTIV for the subject On 05/22/2017 12:33 PM, John Anderson wrote: > Dear

[Freesurfer] estimated Total Intracranial Volume

Dear experts, i want to know if the eTIV can be used to adjust non-morphometric measures like ,diffusion, PET, ASL ,, etc. Can these measures be adjusted to eTIV. if yes what is the correct command to be used? Thank you Jon___ Freesurfer mailing list

[Freesurfer] Optseq2

Hi, I have a question about software input. --ntp 340 --tr 1.8 --psdwin 0 20 1.8 --ev L1 1.6 60 --ev L2 1.6 60 --ev Blank 1.6 15 --evc 1 -1 0 --nkeep 3 --o IAPS --tnullmin 2 --tnullmax 5.6 --nsearch 1 Here is the input that I have provided but it is problematic. Please could you let me

Re: [Freesurfer] Freesurfer Cerebellum Overgrab

I tried to send the email below on May 10, 2017 with screenshots but received an email stating: Your mail to 'Freesurfer' with the subject Freesurfer Cerebellum Overgrab Is being held until the list moderator can review it for approval. The reason it is being held: Message body is

Re: [Freesurfer] Importing external statistical map and overlaying over freesurfer anatomical

Is the BV map a surface or a volume? On 05/16/2017 03:22 PM, Jerry Jeyachandra wrote: > > Hi Freesurfer list, > > I have a statistical map (.nii format) produced from analysis > performed in BrainVoyager that I’d like to register with the > anatomical model produced with Freesurfer’s

Re: [Freesurfer] Contrast matrix regressing out effect of diagnosis and age

yes On 05/19/2017 03:02 AM, Erik Lindberg wrote: > Dear Freesurfer experts, > > I am running a GLM-model in which I have 6 classes (diagnosis) and two > covariates age and variable X). > > I want to look at mean correlation of variable X. > > My contrast matrix is as follows: 0 0 0 0 0 0 0 0 0

Re: [Freesurfer] 3D conversion of Desikan-Killiany Atlas

You can just recon-all the MNI152 On 05/18/2017 08:38 PM, Kwangyeol Baek wrote: > Hi, all. > > Is there a 3D MNeI space version of Desikan-Killiany Atlas? (e.g. a > sample 3D parcellation using MNI152 brain) > Please let me know where I can find it or how I can get it in using > Freesurfer. >

Re: [Freesurfer] local gyrification index (lGI) Error in Design

The problem is that your variable is always0 for the HC group. This creates a regressors of all 0s when using DODS. One way around this is to use DOSS (--fsgd your.fsgd doss) and change the contrast matrix. This may not be the model you want (it will assume that the change due to Antipsychotic

Re: [Freesurfer] lgi vertex coordinate problem

I don't think that freesurfer_surf2voxles is our command is it? In any event, I don't know what you mean about shifts. On 05/19/2017 09:01 AM, Serian doma wrote: > Hi there, > > I am trying to use local gyrification index values for the purpose of > adaptive smoothing. I use recon -all and

Re: [Freesurfer] mri_glmfit-sim output error

Can you add --debug as the first argument and send the terminal output? On 05/19/2017 11:48 PM, Duy Nguyen wrote: > Dear FreeSurfer experts, > > When I try to run mri_glmfit-sim, the output came out like this: > > cmdline mri_glmfit.bin --y lh.gender_age.thickness.10.mgh --fsgd >

Re: [Freesurfer] Thresholding sig.mgh with cluster extent K > 20 voxels

Yes. On 05/22/2017 11:03 AM, Elijah Mak wrote: > Thanks Doug. Just to confirm do I get this voxels number from the > cluster summary text file then? > > Best Wishes, > Elijah > > *Dr. Elijah Mak, Research Associate* > Department of Psychiatry, Old Age Psychiatry Group > University of Cambridge

Re: [Freesurfer] Extracting fMRI mean time series from Desikan ROIs

You can do it that way. You can remove the step of mapping the data into the volume and just pass the native volume to vol2surf and the bbreg registration as the --reg file (instead of --regheader). For mri_segstats, you can spec --avgwfvol lh.fmri_aparc.nii.gz (also I would add --excludeid 0

Re: [Freesurfer] Thresholding sig.mgh with cluster extent K > 20 voxels

Thanks Doug. Just to confirm do I get this voxels number from the cluster summary text file then? Best Wishes, Elijah Dr. Elijah Mak, Research Associate Department of Psychiatry,  Old Age Psychiatry Group University of Cambridge Trinity College, CB21TQ, UK

Re: [Freesurfer] fix topology issue

Hi Paul, are you using version 6? Is this happening on more than one subject or is this subject an outlier? On 05/19/2017 10:28 AM, Bruce Fischl wrote: > Hi Paul > > you need to look at the rh.orig.nofix and rh.inflated.nofix. Typically > something big is wrong like skull attached to brain or

Re: [Freesurfer] How to visualize the result with mri_glmfit and --table aparc flag

beta = MRIread('beta.mgh'); beta.vol will have the pixel data On 05/19/2017 11:04 PM, Duy Nguyen wrote: > Thank you for you quick response Doug > > Please instruct me how I can read out the output file beta.mgh to get > the values from the mri_glmfit output on FreeSurfer. > Thank you for your

Re: [Freesurfer] Thresholding sig.mgh with cluster extent K > 20 voxels

There is not a straight-forward way to do it as mri_glmfit-sim only takes a clusterwise p-value threshold. You can change that until you get 20 voxels. On 05/21/2017 09:48 AM, Elijah Mak wrote: > Hi Everyone, > > How may I threshold the sig.mgh (p<0.001) with a cluster extent K > 20 > voxels?

Re: [Freesurfer] Recon-all error: -autrecon2 unrecognized

there is a typo: it should be "-autorecon2" not "-autrecon2" cheers Bruce On Mon, 22 May 2017, Gwang-Won Kim wrote: Hello FreeSurfer Developers, I saw UserContributions/FAQ of FreeSurfer as following: Q. I have already skull-stripped data. Can I submit it to recon-all? A: If your

Re: [Freesurfer] [How to transform the statistical map from the average surfaces into the individual subject's surfaces]

Hi Jeongsik mri_surf2surf should do the trick cheers Bruce On Mon, 22 May 2017, 김정식 wrote: Dear FreeSurfer experts, Recently, I've been developing the way to detect regions with cortical dysplasia from MRI-negative. So, I compared an individual epilepsy patient's MRI with 30 healthy

Re: [Freesurfer] Installing and enabling cuda

Dear Richard, After compiling in the same way as given in the webpage, I couldn't reboot. It was showing a message that "running low graphic mode". It was not opening the desktop. Then through ctrl+alt+f1, I uninstalled nvida and cuda. Then I could boot the system. Finally I have installed both

Re: [Freesurfer] Recon-all error: -autrecon2 unrecognized

It looks like -autrecon2 is misspelled. It should be -autorecon2 I hope this is helpful. Best regards, Don [Signature0001] Don Krieger, Ph.D. Department of Neurological Surgery University of Pittsburgh (412)648-9654 Office (412)521-4431 Cell/Text From: freesurfer-boun...@nmr.mgh.harvard.edu

[Freesurfer] Recon-all error: -autrecon2 unrecognized

Hello FreeSurfer Developers,I saw UserContributions/FAQ of FreeSurfer as following:Q. I have already skull-stripped data. Can I submit it to recon-all?A: If your skull-stripped volume does not have the cerebellum, then no. If it does, then yes, however you will have to run the data a bit

Re: [Freesurfer] cuda-gpu problem

Dear Richard, The following last line get repeated same way except (%) in the second line pasted below. On the third line "Did not call MRIsetResolution", is it error or normal process? Since repeated many times I thought there is some error. PutOnGPU: Did not reset gca in dst 0270: dt=9.072001,

[Freesurfer] Differences for the longitudinal processing with FreeSurfer 6.0 versus 5.3 ?

Hello everyone, I would like to know if there are big differences between the new verson 6.0 versus the old one 5.3 regarding the recon-all and qcache processing ? Thanks, Best regards, Lisa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Error in hippocampal subfield segmentation

Hi Eugenio Here is the log file. Thanks in advance. Kind regards Mamun On Mon, May 22, 2017 at 7:05 PM, Iglesias Gonzalez, Eugenio < e.igles...@ucl.ac.uk> wrote: > Thanks! Can you please send the log files: recon-all.log and > hippocampal-subfields-T1.log, which can be found in >

Re: [Freesurfer] cuda-gpu problem

On 22 May 2017 at 03:10, Ramesh Babu wrote: > I have attached two documents. One document contains report with -use-gpu > flag which I have interrupted and another document is without -use-gpu flag, > completed without any error. Wherever report differ from normal run

Re: [Freesurfer] Installing and enabling cuda

On 21 May 2017 at 23:40, Ramesh Babu wrote: > Thank you for your reply. I tried to compile by looking FAQ about CUDA in > Ubuntu Ask, but it is get corrupted and I am forced to uninstall both NVIDIA > driver and CUDA. I need help to compile it. Can I get some

Re: [Freesurfer] Error in hippocampal subfield segmentation

Thanks! Can you please send the log files: recon-all.log and hippocampal-subfields-T1.log, which can be found in $SUBJECTS_DIR/[SUBJECT_NAME]/scripts/ ? Cheers, /Eugenio Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London

Re: [Freesurfer] Error in hippocampal subfield segmentation

Dear Eugenio It has been working very well. It stopped working suddenly. It produce two error containing text file within 10 seconds. I tried to install fresh matlab runtime2012b. However, I have not seen any change. The error is bumped as attached. There are no output file except two errors that

[Freesurfer] Antw: Re: Hippocampal subfield segmentation problem

Dear Eugenio, Thank you very much for the prompt reply, it seems like RAM was the key, it works now. Thank you once again. Artyom >>> "Iglesias Gonzalez, Eugenio" 19.05.17 16.48 Uhr >>> Dear Artyom, You’re probably running out of RAM memory in those few cases. How

[Freesurfer] wmsubseg and hippocampal subfield in gtmseg

Dear Freesurfer Experts, We have experiment on functional change based on PET in white matter and found that freesurfer's gtmpvc is very much helpful. We would like to ask if we can get gtmseg to subsegment wm in to gyral based parcellation instead of lobar wm? We know that we can create our

Re: [Freesurfer] Error in hippocampal subfield segmentation

Thanks, Mamun. Do you bump into this error with every subject you process? Also, what’s the output before the error? Cheers, /Eugenio Juan Eugenio Iglesias ERC Senior Research Fellow Translational Imaging Group University College London http://www.jeiglesias.com http://cmictig.cs.ucl.ac.uk/ On