Re: [Freesurfer] ROI NumVert

A difference of 10 out of 500 or 1000 does not both me at all. Why do you need to create your own atlas? It is doable for the cross hemi stuff, it is just difficult. On 10/26/16 10:16 AM, Daya P wrote: Thank you for your help! I created a registration template and atlas from scratch could I

Re: [Freesurfer] Group analysis Cortical Thickness

Check out the group analysis tutorial https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/GroupAnalysis On 10/26/16 7:11 AM, Dev vasu wrote: Dear Freesurfer Group, I would like to perform group analysis for 50 Subjects (25 healthy controls and 25 Subjects with BLVP ) and examine the changes

Re: [Freesurfer] tmp directory not created

which tmp folder? On 10/26/16 11:26 AM, Sneha Pandya wrote: Hi all, I am running recon-all stream for ~200 subjects and after successful run of them I observed that for some of the patients recon-all ran successfully without error but it did not create "tmp" sub-folder. Can anyone please

Re: [Freesurfer] Question about mri_glmfit-sim

Using perm will certainly avoid a lot of questions. You should still use the --2spaces. You changed the threshold from 2.3 to 1.3. This threshold is arbitrary, you don't necessarily need/want a lower threshold for perm. I've been doing some experiments lately, and a threshold of 2.3 with >5mm

Re: [Freesurfer] Fw: Re: surface based analysis for subcortical structures

If you want to use GRF, then I should get you new versions of some of the programs as the volume-based GRF used the Friston 1994 algorithm that was not as accurate as the Worsley 1996 algorithm. I just updated my code last week (better late than never:). But in the end, you probably want to use

Re: [Freesurfer] tkregister2 + mri_vol2vol do not transform

You should run tkregister2 without the --noedit to see if your registration is correct. When you use --regheader, it will compute the registration based on the scanner cooridinates in the mgz files. They apparently have the same coordinates because the matrix is the identity On 10/17/16 11:47

Re: [Freesurfer] Multiple Comparison Question for surface-based analyses

On 10/17/16 2:16 AM, Ajay Kurani wrote: Hi Doug, I had some additional questions regarding multiple comparisons in Freesurfer. 1) Do you correct the left and right hemispheres separately or combine both together for muliple comparison correction? We correct each hemi independently and the

Re: [Freesurfer] tmp directory not created {Disarmed}

when I ran recon-all it created "tmp" folder for some of them whereas skipped for rest. bem label mri scripts src stats surf tmp touch trash Thanks, Sneha *From:* freesurfer-boun...@nmr.mgh.harvard.edu on beh

Re: [Freesurfer] How to get numerical r values from analysis

That is not available from the QDEC window. You will need to run it again after downloading and installing a new mri_glmfit below https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_glmfit when you run QDEC again, it will create a pcc.mgh file in the output folder. This is voxel-wise r-values

Re: [Freesurfer] fsaverage_sym LR-flipchecks

Hi James, this looks like a fairly complicated analysis, and I'm not sure I understand it all. Are the overlays fMRI or thickness results? How did you generate, for example, the top left images? On 10/26/16 3:15 AM, James Roe wrote: ​ Hi Freesurfer experts I have an ultimate goal of perfor

Re: [Freesurfer] tmp directory not created {Disarmed}

create the folder. Regards, Sneha *From:* freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Douglas Greve *Sent:* Friday, October 28, 2016 12:07:13 PM *To:* freesurfer@nmr.mgh.harvard.edu *Subject:* Re: [Freesurfer] tmp

Re: [Freesurfer] values of 0 in the beta.mgh files

If you use the --no-prune flag, then it will consider all subjects at a vertex regardless of whether it is 0 or not. But is this really what you want to do? >>Thank you so much for the reply. Yes I do se now, that single subjects which have certain vertexes with a value of 0 thus excludes t

Re: [Freesurfer] Recon-all Exiting without Error

To answer your question, you need to tell recon-all what to do. Eg, -all On 10/31/16 10:47 AM, Harms, Michael wrote: Hi, Is this just an exercise to try to duplicate the HCP processing? Because we’ve already run all subjects (with released structural data) through FreeSurfer for users. che

Re: [Freesurfer] Creating overlay files automatically

namens Douglas Greve *Verzonden:* vrijdag 28 oktober 2016 17:19 *Aan:* freesurfer@nmr.mgh.harvard.edu *Onderwerp:* Re: [Freesurfer] Creating overlay files automatically We usually create nifti or mgz files to use as overlays both for the volume or the surface. Is this what you mean? On 10/28

Re: [Freesurfer] BBR not recommended for PETSurfer?

Hi Christopher, yes, my position on BBR for PET has changed. I ran an analysis on FDG from an HR+ using BBR and coreg, and the results were not different enough to warrant choosing one over the other. However, coreg performed better on simulated FDG HR+ data, so I'm recommending coreg over BB

Re: [Freesurfer] perl & bbregister conflicts

fyi: the new version of bbregister will use the FS-native mri_coreg, so this problem will disappear On 11/8/16 10:17 AM, Z K wrote: > Thank you for this information. I believe we test against the same > version of fsl (5.0.7). I'll look into it. > > On 11/08/2016 06:32 AM, GREGORY R KIRK wrote:

Re: [Freesurfer] GM ROI list?

We don't currently have that information (ie, tissue type) stored with the ROI. One thing you can do is to run mri_binarize with the --gm option on aparc+aseg.mgz This uses some rules to determine what is GM and creates a mask of GM. You can then feed this into mri_segstats with --mask, and i

Re: [Freesurfer] mapping ROI to surface space

Use mri_surf2surf to convert it to an mgh or mgz file, then use mri_cor2label with the --surf option to convert it to a label On 11/8/16 9:41 AM, Andrews, Derek wrote: > Hi Bruce and Freesurfer developers, > > Thank you. Any suggestions on converting a binary .w file to a label would > be very h

Re: [Freesurfer] GM ROI list?

is the most currently available? ... and, in case it's useful, the explicit version of my mri_binarize (bottom line of the help) is: $Id: mri_binarize.c,v 1.26.2.1 2011/04/08 15:40:50 greve Exp $ Thanks, pt On Tue, Nov 8, 2016 at 11:08 AM, Douglas Greve mailto:gr...@nmr.mgh.harvard.edu&

Re: [Freesurfer] GM ROI list?

yes On 11/8/16 11:51 AM, P Taylor wrote: Ah, cool, that looks like it does the trick-- thanks much. Will that version of mri_binarize be in the next release of FS? Thanks, pt On Tue, Nov 8, 2016 at 11:35 AM, Douglas Greve mailto:gr...@nmr.mgh.harvard.edu>> wrote: Try th

Re: [Freesurfer] GM ROI list?

h the aparc.a2009s+aseg.mgz and aparc+aseg.mgz files, right? Running "mri_binarize --gm ..." on each of those files separately gave the same mask-- I believe this should be a general property? Thanks, pt On Tue, Nov 8, 2016 at 11:57 AM, Douglas Greve mailto:gr...@nmr.mgh.harvard.edu>

Re: [Freesurfer] mapping ROI to surface space

>> Institute of Psychiatry, Psychology & Neuroscience, King's College London >> >> Telephone: +44 (0)20 7848 5701 >> Email: derek.andr...@kcl.ac.uk >> >> >> >> >> >> On 08/11/2016 16:10, "Douglas Greve" wrote: >>

Re: [Freesurfer] GM ROI list?

onding to GM ROIs?) so I can have as secure a set of GM labels as possible? Thanks, pt On Tue, Nov 8, 2016 at 12:29 PM, Douglas Greve mailto:gr...@nmr.mgh.harvard.edu>> wrote: Yes. It just uses a rule on the numbers that it expects to be GM. At some point, I'll add

Re: [Freesurfer] mapping ROI to surface space

Telephone: +44 (0)20 7848 5701 > Email: derek.andr...@kcl.ac.uk > > > > > > On 08/11/2016 16:10, "Douglas Greve" wrote: > >> Use mri_surf2surf to convert it to an mgh or mgz file, then use >> mri_cor2label with the --surf option to convert it to

Re: [Freesurfer] aparcstats2table

Appears to be having problems reading the qdec table. It might be expecting the qdec table to actually variables in it. Can you try adding variables? Also, try it without the --qdec flag instead specifying the subjects with --subjects HC003_1 HC004_1 ... On 11/8/16 8:09 PM, Martin Juneja wrot

Re: [Freesurfer] GM ROI list?

combined set, we can deselect any of the "MatchValues" of WM/CSF/background/etc. to be left with GM? Thanks, pt On Tue, Nov 8, 2016 at 1:32 PM, Douglas Greve mailto:gr...@nmr.mgh.harvard.edu>> wrote: Actually, what it does is to binarize all the labels that it t

Re: [Freesurfer] mri_gtmpvc error: failed tissue type check

Was gtmseg.mgz created with the gtmseg script? On 11/9/16 4:43 AM, Donatas Sederevicius wrote: Dear Freesurfer community, An error has occured while applying PET partial volume correction using mri_gtmpvc. A snippet from the log file: Reading /projects/PET/recon/ID247/mri/gtmseg.lta Replac

Re: [Freesurfer] nuisance dichotomous variables

I'm not sure what you mean. Dichotomous variables can be used. Our tutorial has an example of using gender. On 11/9/16 5:05 AM, Dominic Dwyer wrote: Dear FS experts, Sorry for my confusion here, but I'm wondering why dichotomous nuisance variables (e.g., gender) can't be used in qdec? I wa

Re: [Freesurfer] Area after fsaverage resample

The "area" of a vertex is the average area of the triangles around the vertex. In fsaverage space, a vertex will map back to a given vertex in the individual subject, so the area of the vertex gets transferred back to fsaverage. And, yes, the area is measured in mm2. On 11/8/16 8:45 PM, Lac

Re: [Freesurfer] dtrecon

No, you can use version 6.0 dt_recon with anat analyses from any FS version On 11/12/16 3:26 PM, John Anderson wrote: Dear Freesurfer experts, I want to analyze DTI data using the command *dt_recon --i dwi.nii --b bvals bvecs --s subj1 --o /subj1* Under Fressurfer 5.3, the analysis fail showing

Re: [Freesurfer] Voxel time series after nuisance regressors removal using fsfast

Run it with -svres. This will force it to save the residuals. They will be in a folder called res (I think) in the output analysis folder On 11/13/16 3:48 AM, Ladan Shahshahani wrote: Dear fsfast users, I've just started to use fsfast for resting state fMRI data processing. I wonder if I coul

Re: [Freesurfer] Cluster Color

On what? Please include previous correspondence so that we have context. On 11/15/16 9:10 AM, Timothy Hendrickson wrote: It seems that this message has been ignored. I really do need an answer on this. -Tim Timothy Hendrickson Department of Psychiatry University of Minnesota Office: 612-624-

Re: [Freesurfer] Freesurfer 6 beta testing: mri_glmfit-sim error

Looks like the most up-to-date version of mri_surfcluster did not get into the distribution. Try this one https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_surfcluster On 11/18/16 9:06 PM, Elijah Mak wrote: Hi Freesurfer Team, I came across the following error while running mri_glmfit-sim

Re: [Freesurfer] fsaverage_sym LR-flipchecks

subj1_flipped >>>> - smoothing and analysis performed on individual surface (with --self) >>>> >>>> >>>> The images below are the respective analyses resampled onto the >>>> surface in which the analysis was not performed >>>> >&g

Re: [Freesurfer] Help with Opseq: Setting Parameters

Not really. You can force there to always be a NULL with --tnullmin. You can also specify the maximum duration of the null event with --tnullmax; this should indirectly cause there to be more instances where nulls appear between non-nulls. On 11/21/16 1:17 PM, Leshin, Joseph wrote: Greeting

Re: [Freesurfer] ASL processing in Freesurfer?

No, not really. If you're not doing anything fancy (eg, just computing mean of tag-control) and mapping to the surface, it is easy enough to do (mri_concat --paired-diff --sum, then bbregister to register to the anat, then mri_vol2surf or mris_preproc to map to fsaverage, then mri_glmfit and mr

Re: [Freesurfer] Demeaning variables

It comes down to the contrast you care about. If you want to look at the difference in mean thickness between the groups regressing out the effect of age, then demeaning can make a big difference. If this is what you want, then you need to do the analysis in two stages. First run with DODS and

Re: [Freesurfer] Demeaning variables

drigo *De:* freesurfer-boun...@nmr.mgh.harvard.edu en nombre de Douglas Greve *Enviado:* martes, 29 de noviembre de 2016 07:33:47 p. m. *Para:* freesurfer@nmr.mgh.harvard.edu *Asunto:* Re: [Freesurfer] Demeaning variables It comes

Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz

I did not. You should have had an opportunity to enter an email address of the recipient. You can use my email On 12/5/16 6:35 PM, Marianna Riello wrote: > I uploaded the dicom mosaic on Martinos Center. > I am wondering whether you received it > > -Original Message- > From: freesurf

Re: [Freesurfer] Volumetric Group Analysis: asegstats2tbale result to plot a z-score map for the segmentation

This is a tricky thing to do. I've created a matlab file to help, which you can get from here: https://gate.nmr.mgh.harvard.edu/safelinks/greve/annotval2surfoverlay.m Look at the help for an example on how to use it. You will have to specify the list of ROI names and the corresponding list o

Re: [Freesurfer] mri_convert dcm 'Mosaic' 2 mgz

ves me an error. >> Check attachment. >> >> -Original Message- >> From: freesurfer-boun...@nmr.mgh.harvard.edu >> [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Douglas Greve >> Sent: Tuesday, December 6, 2016 10:23 AM >> To: freesurfer@nmr.mgh.harvard.e

Re: [Freesurfer] Odd Extremely High/Low Banding of Functional Values in Volume

sorry, I don't remember this case. please repost with our previous correspondence included On 12/12/16 5:40 PM, Dowling, Kevin Francis wrote: Hi Doug, Thank you for your note and my apologies for a delayed response. To create the sig.mgh file we used a volume specific mri_glmfit analysis, o

Re: [Freesurfer] (no subject)

To get the t-score, compute the square root of the F, like fscalc F.mgh sqrt -o t.mgh You can then get the clusters with mri_surfcluster --in t.mgh --thmin t-threshold --sign sign --no-adjust --sum sumfile --ocn ocn.mgh ocn (output cluster number) will be a map with the custer number as the

Re: [Freesurfer] mris_apply_reg

here you go ... https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_apply_reg On 12/9/16 4:01 PM, Matthew Defenderfer wrote: Hi All, I am trying to mirror labels across hemispheres and found various threads using mris_apply_reg. Unfortunately the version of that command I have does not rec

Re: [Freesurfer] recon-all -s -localGI

The LGI routines run matlab (even though you never actually run any matlab commands yourself). But you have to make sure that matlab knows where the LGI matlab routines are. To do this you must modify your matlab ~/matlab/startup.m file to add the path to the LGI routines to your path. To do th

Re: [Freesurfer] Label creation

Not that easy. I would do it by selecting a vertex that is close to the coordinate you want, then 1. Create a surface overlay with all vertices = 0 except your chosen vertex mri_volsynth --template $FREESURFER_HOME/fsaverage/surf/lh.thickness --delta vertexno 0 0 0 --o delta.mgh 2. Smooth

Re: [Freesurfer] recon-all -s -localGI

/BugReporting Do you know why it's still not working? Thanks again and best wishes André *Von:* freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Dou

Re: [Freesurfer] correlation in mri glmfit controlling for 2 categorical variables and 1 continuous variable

Does this cover your situation? https://surfer.nmr.mgh.harvard.edu/fswiki/Fsgdf4G1V On 12/9/16 9:54 AM, Emmanuel Nwosu wrote: Hi All Am not sure if I can do this in mri glmfit I want to investigate the relationship between cortical thickness and a continuous variable (A) while accounting fo

Re: [Freesurfer] project 3D ROI onto flatmap

You will need a registration between the space where the ROIs are and the anatomical. We usually do this with bbregister, but you will need to identify a volume that is in the ROI space that has anatomical contrast so that the registration can be done (ie, dont use the ROI mask for registration

Re: [Freesurfer] Demeaning variables

) instead of four (malecontrol, malepatient,….) , or it is > better to continue as I’ve been doing, controlling for the effect of > gender. > > > Thanks for your help! > > > Rodrigo > > >

Re: [Freesurfer] recon-all -s -localGI

*Von:* freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu]" im Auftrag von "Douglas Greve [gr...@nmr.mgh.harvard.edu] *Gesendet:* Dienstag, 13. Dezember 2016 22:53 *An:*

Re: [Freesurfer] (no subject)

Hi Sadhana, this has been answered several times. Are you not getting the replies from the list? On 12/16/16 6:13 PM, Sadhana Singh wrote: Hello FreeSurfer Developers, I'm running the recon-all on my subjects data as described in freesurfer tutorial (https://surfer.nmr.mgh.harvard.edu/fswiki/

Re: [Freesurfer] Missing values in fsgd file

no, sorry, you'll have to remove those data sets or run an analysis that does not rely on that parameter On 12/20/16 11:05 PM, Jennifer Szeto wrote: > Hi freesurfer experts, > > I am trying to run some mri_glmfit analyses on freesurfer5.3. However there > are some missing values in some of m

Re: [Freesurfer] Fwd: Registering ASL-CBF maps to fsaverage

Sorry for the delay On 12/21/16 12:15 AM, neuroimage analyst wrote: Hi, I am attaching this message again and I wI'll appreciate if somebody could kindly comment on the approach. Thanks Regards -VM -- Forwarded message -- From: "neuroimage analyst"

Re: [Freesurfer] mri_glmfit-sim

The 2nd one On 12/31/16 6:06 AM, std...@virgilio.it wrote: Hi list, which is the correct option, please? 1- mri_glmfit-sim --glmdir my-glm.wls --cache 1.3 abs --cwpvalthresh .0166 --3spaces 2- mri_glmfit-sim --glmdir my-glm.wls --cache 1.3 abs --cwpvalthresh .05 --3spaces Thanks Best reg

Re: [Freesurfer] drawing circle around vertex on surface

There is no one command that will do it. You can do it in matlab, something like a = MRIread('spike.mgh'); a.vol = a.vol/a.vol(yourindex); MRIwrite(a,'spike.rescale.mgh'); Or you can get the vertices and values with mri_convert spike.mgh --ascii+crsf to get all the vertices and their val

Re: [Freesurfer] surface based analysis (projfrac)

When you say in the corpus callosum, do you mean in WM? The surface-based analysis is only for cortical GM. If you mean in GM near the CC, then the analysis is appropriate. The projfrac parameter sets the sampling location between the white and pial surfaces where 0.5 means half way. On 1/10

Re: [Freesurfer] ERROR: fast_selxavg3() failed\n

It looks like your FS_OCTAVE_BIN env variable is set to that bin folder. This variable should be set to the octave executable On 1/10/17 7:34 AM, Michael Schirner wrote: > Dear experts, > > I'm attempting to perform step 6 in the FsFastTutorialV5.1 > (https://surfer.nmr.mgh.harvard.edu/fswiki/Fs

Re: [Freesurfer] ribbon volumes

Almost. This will include medial wall voxels that are not GM. It will also not include subcort GM. It is better to use aparc+aseg.mgz and merge the GM ROIs together. On 1/15/17 1:01 AM, Zhivago wrote: Hi, Are the lh.ribbon & rh.ribbon volumes the GM estimate from reconall? Can I used these

Re: [Freesurfer] mri_glmfit error: negative DOF -10

It usually means that the number of subjects in the input is less (10 less) than the number of regressors. It looks like you have about 14 input subjects and 24=6*4 regressors. You need to add subjects or remove regressors (ie, classes or covariates) doug On 9/18/13 11:41 AM, Robert Schulz wro

Re: [Freesurfer] Qdec analysis --> Don't use DOSS with QDEC

Hi Marie, On 9/20/13 4:30 PM, Marie Schaer wrote: > Hi Doug, > > I'm jumping in the discussion because I was a bit scared with your previous > email mentioning that this DOSS bug affects all FreeSurfer's versions. Does > that also affect statistical analyses computed with mri_glmfit using the

Re: [Freesurfer] ACFFWHM for surface-based analyses in FSFAST?

I think even in single subject data it will not be much of an effect. I looked at it a little bit when I first programmed it. doug On 9/20/13 6:55 PM, Caspar M. Schwiedrzik wrote: Hi Doug, thanks for the response. I will also be looking at some single subject data, that's why I am asking. D

Re: [Freesurfer] qdec analysis and covariates

what post? Can you include it in the email so that I know what you are referring to? doug On 9/23/13 7:06 AM, Anita van Loenhoud wrote: > Hi, I have a question related to this post. Besides an age-group > interaction, wouldn't it also be neccesary to check for an age-gender > interaction? >

Re: [Freesurfer] Problem in final analysis

Hi Carina, run recon-all -s subject -qcache for each subject and this will create the file doug On 9/28/13 5:37 AM, car...@van-vlodrop.de wrote: Dear freesurfer community, we are conducting cortical-thickness analysis using freesurfer-4.4.0 and have been experiencing some problems with t

Re: [Freesurfer] LGI mean value per hemisphere

use --slabel subject lh $SUBJECTS_DIR/subject/label/lh.cortex instead of --annot doug On 10/6/13 5:16 PM, Jane Garrison wrote: Hi I have a question related to calculation of the local gyrification index using FreeSurfer. I have computed the LGI and checked the results successfully. I ca

Re: [Freesurfer] symmetric template in freesurfer

Yes, it is released. See https://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi doug ps. Please remember to post to the list. Thanks! On 10/6/13 11:10 PM, Xinian Zuo wrote: Hi Doug -- Hope all is well. I am writing to follow up my previous question about the symmetric templates of brain surfaces. I

Re: [Freesurfer] Error with bbregister (using T2 to refine pial surface)

here you go ftp://surfer.nmr.mgh.harvard.edu/transfer/outgoing/flat/greve/fslregister On 10/9/13 5:22 AM, Sophie Maingault wrote: Dear FS experts, I'm trying to use T2 weighted image to refine the pail surface. I have this error message : ERROR: you must have the FSLDIR environment variable d

[Freesurfer] Fwd: OHBM 2014 Call for Council Nominations

Original Message Subject:OHBM 2014 Call for Council Nominations Date: Mon, 14 Oct 2013 09:50:14 -0500 From: i...@humanbrainmapping.org Reply-To: i...@humanbrainmapping.org To: gr...@nmr.mgh.harvard.edu Dear OHBM Mem

Re: [Freesurfer] Qdec taking a very long time

Did you run recon-all with -qcache? If not, then it is having to preprocess all the data (ie, sample to common space and smooth). It will take the same amount of time with -qcache, but it will store (ie, cache) the results so that it will only take a few minutes if/when you run it again. Still

Re: [Freesurfer] How do you create labels from binary masks?

I think you need to use mri_cor2label (not very well named:) doug On 10/16/13 4:24 PM, Marcos Martins da Silva wrote: Hi, Freesurfers. I need to create some labels from binary masks. Sometime ago I read a post (https://mail.nmr.mgh.harvard.edu/pipermail//freesurfer/2013-October/033783.html )

Re: [Freesurfer] aparcstats2table error

Hi Corinna, is it just that subject or does it happen on more? Can you send me the stats file? doug On 10/17/13 3:55 PM, Corinna Bauer wrote: Hi; I want to put cortical thickness in a table format and am getting an error. command: aparcstats2table --subjectsfile symmetry_subjects.txt --he

Re: [Freesurfer] How do you create labels from binary masks?

help): mri_cor2label --i aseg.mgz --id 12 --l left-putamen.label This label also shows only -1 as vertex number. Could you please explain me what do I need to do to get the vertex numbers in the label file as output of mri_cor2label? Cheers, Marcos Em Qua, 2013-10-16 às 20:34 -0400, Douglas

Re: [Freesurfer] missing eTIV in asegstats2table

Hi Daniel, what is this in reference to? If this is a follow up on a previous thread, please include the rest of the thread and the file in the same email. I go through way too many emails to keep track of who's doing what. thanks! doug On 10/23/13 4:13 AM, Daniel Ferreira wrote: Dear Dou

Re: [Freesurfer] Power of MRI machine

The field strength is in the dicom header. If you have a dicom file, just run mri_probedicom --i dicomfile This will print out a lot of info including the field strength doug On 10/27/13 9:57 PM, Muhammad Naveed Iqbal Qureshi wrote: Dear Community, Is it possible to detect the scanning power

Re: [Freesurfer] Betreff: Error “mri_segstats will not calculate Supratentorial due to missing ribbon.mgz file”

I have put patches for mri_segstats here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/ this should fix the problem doug On 11/3/13 12:09 PM, jana dinges wrote: Dear freesurfer community, unfortunately there was a mistake in the previous mail. Please find attached the c

Re: [Freesurfer] new version of mri_segstats

I've put new versions here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/ doug On 11/4/13 7:09 AM, Matura, Silke wrote: Dear Freesurfer community, we are doing cortical thickness analyses with Freesurfer version 5.3.0 in a Linux environment. In order to do the autorecon

Re: [Freesurfer] Creating group average ROI

I would convert them to a binary mask (0,1) then average the masks together. Each vertex would then be the "probability" that a given vertex was in the ROI. You can convert the label to a binary mask with a second call to mri_label2label (--outmask option) doug On 11/4/13 8:47 PM, Miggy Ch

Re: [Freesurfer] acquisition in 1 session vs 2 sessions

I think the only thing you would have to worry about is the fMRI since the way the subject reacts to the task (or state of subject during rest) might change depending upon how long he/she has been in the scanner. Why not do the fMRI at #3? Then each population would be in the scanner for the

Re: [Freesurfer] Choi2012 convert to FSL MNI152 2mm

Is the Choi2012 volume in fsaverage/mni305 space? If so, then the 2nd command is the right one. Use mri_binarize with the --match option to create separate masks. doug On 11/11/13 2:24 PM, Kathy L. Pearson wrote: > To convert an example Choi2012 file to FSL 2mm space in FreeSurfer 5.2, I > ha

Re: [Freesurfer] aparcstats2table question

I think you just need the qdec table. doug On 11/11/13 11:27 AM, Jonathan Holt wrote: > Hi FS experts, > > I’m about to run aparcstats2table for a longitudinal study, and I’m wondering > seeing as I’ve already written a longitudinal qdec table that includes > subject IDs under the fsid column,

Re: [Freesurfer] question about atrophy and FS-FAST

No, there is nothing special you need to do. FSFAST will sample halfway between the white and pial surfaces which will be as good as you can get for atrophied brains. doug On 11/11/13 11:47 AM, Mario Ortega wrote: Hello Freesurfer group, I have a general question about the Freesurfer pip

Re: [Freesurfer] aparcstats2table for multiple labels

The only way to do what you want is to combine the labels into an annotation file (mris_label2annot), then run mris_anatomical_stats on the annot, then you can run aparcstats2table on the output of that. This may or may not be easier than doing what you are already doing. doug. On 11/10/13 3:

Re: [Freesurfer] Getting substantially different Etiv for same patients for consecutive scans

Did you check the registrations to see if either or both are inaccurate? As you point out, the eTIV is based on the registration an not an actual count of voxels inside the skull. It may be the case that one time point has more or less neck than the other which could skew the registrations si

Re: [Freesurfer] Fixed-Effects Analysis carried out by mri_glmfit

Hi Clark, mri_glmfit should work fine. If you have the ROIs in a volume format (eg, nifti or mgh) you can run mri_concat on them to create a stack, then just pass the stack to mri_glmfit with the --y flag (also add --no-est-fwhm). If you don't have them in a volume format, you can create a vol

Re: [Freesurfer] Fixed-Effects Analysis carried out by mri_glmfit

Clark, it sounds like what you did (ie, combine different subjects into one folder) would be tricky to analyze correctly because FSFAST will try to register them to the same subject. I could think of a way to do it, but it would be complicated. What is the test that you want to do? An F test i

Re: [Freesurfer] can I run Monte Carlo simulation without calling mri_glmfit

The easiest thing to do is to create a "fake" contrast in the folder where you ran simulation and populate it with the needed files named in the proper way. The only important one will be sig.mgh, but the others have to be there (you can just copy them from some other folder). Copy the CSD fi

Re: [Freesurfer] freeview, mris_preproc, mri_surf2surf, mri_glmfit: wrong home directory

you don't need to supply the full path to the inputs of mris_preproc, but you must for the output of mris_preproc as well as the input and output of surf2surf and glmfit On 11/28/13 1:25 PM, Laura Taylor wrote: Thanks, Bruce... Do you know if you also have to specify the full path for th

Re: [Freesurfer] major lobes

The commands look right and it sounds like you might have the right result. What do you mean you are getting a detailed WM + GM segmentation? If you just load freeSurfer_lobes.nii.gz into tkmedit, the label names will be all messed up because you don't have the proper color table, but you shou

Re: [Freesurfer] Within group hemisphere comparison in QDec

yep, we have an existing stream complete with documentation and a publication you can cite! http://surfer.nmr.mgh.harvard.edu/fswiki/Xhemi On 11/30/13 12:59 PM, krista kelly wrote: Hello, I need to do a within group hemisphere comparison to see if there are any hemisphere asymmetries in a

Re: [Freesurfer] Volume differences after corrections

Hi Gari, this is expected because of the way that we estimate intracranial volume (based on registration to talairach space). But even in theory, you are only changing what is brain and not what is skull so eICV should not change. doug On 11/28/13 11:52 AM, Garikoitz Lerma-Usabiaga wrote:

Re: [Freesurfer] Fwd: converting to fsaverage space

Don't go through fsaverage. Instead use mni152reg to create a registration matrix from an individual to the 152 (stored in $SUBJECTS_DIR/$subject/mri/transforms). Then use the command below with this registration matrix instead of mni152.register.dat doug On 11/27/13 2:57 PM, Paul Beach wr

Re: [Freesurfer] FW: recon -all in FS version 5.3 CentOS 6

Others (Nick, Zeke) correct me if I'm wrong, but you will get different answers with the two operating systems, so I would just analyze them on a single OS. doug On 11/27/13 3:46 PM, pablo najt wrote: Dear FS experts, I am forwarding a message I sent yesterday that my got lost in the lon

Re: [Freesurfer] Within group hemisphere comparison in QDec

hen using that in place of (subject list). This didn't work. You're half way there, just set subjectlist = `cat subjectlistfile` where subjectlistfile is the file that you created (which can be called anything) doug Thanks again! On Sat, Nov 30, 2013 at 2:34 PM, Douglas Greve mailto

Re: [Freesurfer] possible pial surface editing

Is this happening systematically? Eg, always on the left side? Or both sides? doug On 12/5/13 3:35 PM, krista kelly wrote: Hi Gen, I'm having the same problem right now with one participant where the pial matter border doesn't extend enough out to the edge of the cortex. Did you try add

Re: [Freesurfer] Significance of value in sig.nii file under 'polar' directory

To get the F test, you will need to put the runs from both sessions in the same bold folder (and make sure to use -per-run registration) doug On 12/5/13 4:42 PM, Cesar Echavarria wrote: Thanks for your help Doug. That cleared things up. One more question, I want to average over 2 of these

Re: [Freesurfer] Patch for -autorecon2

Sorry, I thought I had updated that link. Use this one and download the program for your OS ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/5.3.0-patch/ On 12/5/13 3:42 PM, Isabelle Deschamps, Miss wrote: > I tried the link, but when I click on it, I get the following error > > ALERT 550

Re: [Freesurfer] mri_convert Siemens .IMA error

This may be a known problem. What version of FS are you using and what is your platform? doug On 12/5/13 3:26 PM, prasser wrote: Thanks, but the orientation shift appears as a skew. Also, we don't have any fiducial markers for this group of scans so it would be a little tricky to confirm

Re: [Freesurfer] Cortical thickness values of significant clusters

That is the right file to use, and one would expect to see significant results. Are you sure you are using exactly the same model? If you have matlab, I can give you some code to do the analysis using the exact model that mri_glmfit uses. doug On 12/9/13 10:43 PM, Sinead Kelly wrote: D

Re: [Freesurfer] viewing the atlas?

Do you mean you want to view it in the volume or the surface? If you want to load it as a volume, you can try using the aparc+aseg.mgz in the fsaverage folder doug On 12/9/13 5:26 PM, Gregg, Brian E. wrote: Hello, I'm looking for a way to view the Desikan-Killiany atlas. I'd like to ope

Re: [Freesurfer] mri_glmfit error

On 12/18/13 10:26 PM, Rujing Zha wrote: Hi Doug and others, Thanks Doug. I modifiled my number of class in the fsgd which can be got in the attachment. And I am confused with 3 problems: 1st: Is what I modified proper? Yes 2nd: How can I deal with my high correlation between age and edu? If

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