Re: [Freesurfer] Flipped left to right hemisphere subjects

Is the volume actually left-right reversed? From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Lutz,Olivia (BIDMC - Psychiatry) Sent: Monday, August 20, 2018 4:55:24 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Flipped left to right

Re: [Freesurfer] ERROR: dimension mismatch between X and contrast

You have 3 groups and 2 covariates, so you will have 3*(2+1)=9 regressors, in this order ADHD-offset COM-offset TD-offset ADHD-Age COM-Age TD-AGE ADHC-IQ COM-IQ TD-IQ You will need to have a single value for each regressor in your contrast matrix, meaning that you should have 9 values. You have

Re: [Freesurfer] tksurfer-sess frame time course question

answwers below On 09/27/2018 05:44 AM, 伊藤匠吾 wrote: > > > Hello, > > I am new to FreeSurfer. > > I conducted an experiment with event-related design. > There were eight non-fixation conditions. In every trial, a simple > stimulus was presented for about 1.5 sec, and the subject made a > button

Re: [Freesurfer] Reporting Cohen's D for a significant cluster

This is the behavior in 6.0. It has been fixed in the deev version. I think it is possible to download just the dev version of freeview. Otherwise, you could do your computation in matlab with c = MRIread('cohensd.mgh'); c.vol(vertexno+1) On 09/26/2018 02:34 PM, Maksimovskiy, Arkadiy wrote: >

Re: [Freesurfer] nu_correct disk i/o issues

Not that I know of, but this is not a native FS script, it comes from the MNI, so it could be doing something we don't understand. Can you do an experiment for us? Can you run it outside of the container using reprozip (or something equivalent) to see all the files it touches? On 10/5/18 5:31

Re: [Freesurfer] Definition of circular label centered on peak vertex

you can create a label with just that vertex, then use mri_label2label to dilate it, then use mri_segstats specifying the label with --slabel, using beta as input (--i), and specifying the output as --avfwf. Run it with --help to get more info On 10/5/18 11:10 AM, Milde, Christopher wrote:

Re: [Freesurfer] Ynt: Ynt: Desikan Atlas in MNI Space

------------ > *Gönderen:* Greve, Douglas N.,Ph.D. adına > freesurfer-boun...@nmr.mgh.harvard.edu > > *Gönderildi:* 11 Ekim 2018 Perşembe 18:26 > *Kime:* freesurfer@nmr.mgh.harvard.edu > *Konu:* Re: [Freesurfer] Ynt: Desikan Atlas in MNI Space > I'm not sure what y

Re: [Freesurfer] Ynt: Desikan Atlas in MNI Space

I'm not sure what you are trying to do. Do you want to map the vbm results to the surface and visualize the aparc (desikan atlas) or do you want to map the aparc into the vbm volume? On 10/11/2018 09:59 AM, ece ulug wrote: > > External Email - Use Caution > > Hi, > > May be i cannot

Re: [Freesurfer] mri_watershed Error

can you send the recon-all log file? On 10/11/2018 11:22 AM, Boris Rauchmann wrote: > > External Email - Use Caution > > When I run recon-all i get the follwing error message: > >  mri_watershed Error: >  GLOBAL region of the brain empty ! > Linux 02f92500bcfb 4.15.0-36-generic

Re: [Freesurfer] FreeSurfer Errors

On 10/11/18 1:58 PM, Sparsh Jain wrote: External Email - Use Caution Hey! I have recently started using FreeSurfer. I have encountered multiple errors over the past few days, and I would like to mention them all. 1. While testing the installation, the code ran for roughly 4-6 hours

Re: [Freesurfer] create label from cluster obtained with mri_glm-fit-sim

, Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> wrote: Which subject did you load it on? It must be fsaverage. Can you send the terminal output and command line? On 10/03/2018 11:31 PM, Ting Li wrote: External Email - Use Caution Dear Freesurfer Expert, I have figur

Re: [Freesurfer] create label from cluster obtained with mri_glm-fit-sim

; Dear Dr. Douglas, >> >> I can load the label, but some clusters have branches. Some of >> them are just looks fine. Do you know the reason? Thanks a lot. >> >> Regards, >> Ting >> >> >> >> >>> On Oct 12, 2018,

Re: [Freesurfer] qdec analysis with more than 2 covariates

You cannot use QDEC. For this case you'll need to use the "command line" stream. You'll need to start by creating an FSGD file https://surfer.nmr.mgh.harvard.edu/fswiki/FsgdExamples On 10/15/18 10:15 AM, vittal korann wrote: External Email - Use Caution Hi Doug, Recently I started

Re: [Freesurfer] Raw Data for Clusters

try mri_segstats --i y.mgh --seg mc-z.abs.th13.sig.ocn.mgh --avgwf mc-z.abs.th13.cluster.ocn.dat --excludeid 0 On 10/17/2018 12:57 AM, WON JONG CHWA wrote: > > External Email - Use Caution > > Dear FreeSurfer Experts, > I am running Qdec 1.4 and I want to extract raw data (in this case,

Re: [Freesurfer] QDEC analysis with more that 2 fixed factors

You cannot use QDEC for this. You must use the "command line" stream, ie, create your FSGD file, run mris_preproc, smooth, run mri_glmfit, then mri_glmfit-sim. See the tutorial on the wiki. On 10/17/2018 01:30 PM, Azeez, Azeezat wrote: > > External Email - Use Caution > > Hello, > > I

Re: [Freesurfer] FreeSurfer Errors (2)

can you send the command-line output as text? On 10/16/2018 11:12 AM, Sparsh Jain wrote: > > External Email - Use Caution > > Hey! > I sent two responses on Friday. The second response was bigger than 1 > MB so it awaited moderator approval. I don't know if you received it > eventually.

Re: [Freesurfer] Nonsensical Vertex Coordinates, please help with interpretation

When you look at the vertex in matlab, are you correctly accounting for the fact that FreeView uses 0-based indexing and matlab uses 1-based? Eg, vertex 234741 in Freeview would be 234742 in matlab. You seem to be using 234740 in matlab below On 10/15/2018 05:11 PM, Bruss, Joel E wrote: > >    

Re: [Freesurfer] qdec analysis with more than 2 covariates

That looks like the terminal output for qdec. You cannot use qdec with your design. If you have questions about the FSGD, I'll be happy to answer them. On 10/16/2018 11:00 AM, vittal korann wrote: > > External Email - Use Caution > > Hi Doug, > > Thank you for your response. > I tried

Re: [Freesurfer] create label from cluster obtained with mri_glm-fit-sim

Li wrote: > External Email - Use Caution > > The annot file loaded successfully and without any branches. Thanks a lot. > > Ting >> On Oct 15, 2018, at 2:22 PM, Greve, Douglas N.,Ph.D. >> wrote: >> >> Click on the surface file name in the uppe

Re: [Freesurfer] [External] Re: Nonsensical Vertex Coordinates, please help with interpretation

atch up to what I can see in > FreeView. > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Greve, Douglas > N.,Ph.D. > *Sent:* Tuesday, October 16, 2018 1:48:14 PM > *To:* freesurf

Re: [Freesurfer] fsfast preproc-sess: viewing preproc surface outputs

You can load them in freeview through tksurferfv, something like tksurferfv fsaverage lh inflated -aparc -ov fmcpr.odd.sm5.fsaverage.lh.nii.gz There's not much to see:) On 10/16/2018 03:00 PM, Jacob Matthews wrote: > > External Email - Use Caution > > Hi FS Team, > > We are running our

Re: [Freesurfer] Surface-based analysis of tfMRI

? On Mon, 22 Oct 2018 at 17:12, Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> wrote: If you do all the preprocessing yourself, then store the output in the run folder with a certain name, fmri-denoised.nii.gz, then when you run mkanalysis-sess specify -funcstem fmri-denoised and p

Re: [Freesurfer] resampling data onto cortical surface

; so that it is in the freesurfer space but not scaled and not changed > from float to uchar, correct ? > > > thanks > > > greg > > -------- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu >

Re: [Freesurfer] Surface-based analysis of tfMRI

If you do all the preprocessing yourself, then store the output in the run folder with a certain name, fmri-denoised.nii.gz, then when you run mkanalysis-sess specify -funcstem fmri-denoised and proceed as norm. On 10/22/2018 04:08 PM, Zhi Li wrote: > > External Email - Use Caution > >

Re: [Freesurfer] resampling data onto cortical surface

Use --s subject instead of --reg (run mri_vol2vol with --help to get more info). btw, if you have multi echo data, you are probably measuring R2*, not R1. On 10/22/2018 12:55 PM, GREGORY R KIRK wrote: > > External Email - Use Caution > > > I have R1 values that I want to resample onto

Re: [Freesurfer] Using a .asc file as overlay in freeview/tksurfer

Not sure. Can you use mris_convert to convert the asc back to a curv file? On 10/15/2018 11:20 AM, Worker, Amanda wrote: > > External Email - Use Caution > > Hello, > > > I am trying to overlay a .asc file in either freeview or tksurfer, but > so far having no luck. > > > As practice and

Re: [Freesurfer] Surface-based analysis of tfMRI

:08, Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> wrote: Actually, if you just store the denoised data as f.nii.gz, then run preproc-sess it should do ok. It will do motion correction, but it should not really do any thing if MC is already done. Just make sure that the ima

Re: [Freesurfer] Running DICOMS versus FreeSurfer5.3 Output

If you have edits you want to save, then you can re-run over 5.3. It should work regardless, but it will be a little cleaner if you start from scratch. On 10/18/18 4:34 AM, Scheffler, F, Mev [fre...@sun.ac.za] wrote: External Email - Use Caution Dear FreeSurfer

Re: [Freesurfer] Mapping a custom measure to the pial surface of fsaverage

You can use preproc-sess and specify the --meas flag. Run with --help for more info. On 10/18/18 2:08 PM, ts...@rcmd.org wrote: > External Email - Use Caution > > Dear FreeSurfer experts, > > I have created a custom measure on the pial surface of a number of subjects, > and I would

Re: [Freesurfer] Physiological Noise Regression from rsMRI

You will just need to create a text file with one or more columns, one for each regressor put this in the run folder (same folder where the raw data are). When you run mkanalysis-sess, add -nuisreg filename N where N is the number of columns you want to include On 10/18/18 10:34 AM, Meisler,

Re: [Freesurfer] QDEC analysis with more that 2 fixed factors

Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> wrote: You cannot use QDEC for this. You must use the "command line" stream, ie, create your FSGD file, run mris_preproc, smooth, run mri_glmfit, then mri_glmfit-sim. See the tutorial on the wiki. On 10/17/2018 01:30 PM, Azee

Re: [Freesurfer] FreeSurfer error at selxavg3-sess

Not sure what the problem is. The "unrecognized" warning is not a problem. What is your mkanalysis-sess command line? What version of FS are you running? You can try just deleting the LH and re-running mkanalysis and selxavg On 10/20/18 12:33 PM, elahe' yargholi wrote: External Email -

Re: [Freesurfer] errors running mri_glmfit

You have no subjects in the DIATD-DEVC-sexM class On 10/18/18 1:53 PM, Azeez, Azeezat wrote: External Email - Use Caution Hello I keep getting the same error and am not sure how to address the issue. I have attached the design matrix and the FSGD file and contrast file of interest

Re: [Freesurfer] Surface-based analysis of tfMRI

in preproc-sess, -mcin, -stcin, etc. Sorry I am a beginner of FreeSufer and not clear about some terms such as 'stem' in both preproc-sess and mkanalysis-sess. On Tue, 23 Oct 2018 at 11:09, Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> wrote: Yes. When you run mkanalysis-sess, y

Re: [Freesurfer] Physiological Noise Regression from rsMRI

, should this happen before or after skull-stripping? Best, Steven From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D.

Re: [Freesurfer] Physiological Noise Regression from rsMRI

r-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <mailto:dgr...@mgh.harvard.edu> Sent: Tuesday, October 23, 2018 12:12:39 PM To: freesurfer@nmr.mgh.harva

Re: [Freesurfer] How to combine and divide surface-based fMRI data?

ted file, it will only skip the first 4 time points of the > 1st run in this file. > > In addition, if my task design is event-related, do I need to set the > duration of each stimulus as 0? > > Thanks and best > > On Wed, 7 Nov 2018 at 12:59, Greve, Douglas N.,Ph.D. > m

Re: [Freesurfer] How to combine and divide surface-based fMRI data?

If so, could you please > give me a example? > > Thanks and best, > > Zhi > > > On Wed, 7 Nov 2018 at 10:16, Greve, Douglas N.,Ph.D. > mailto:dgr...@mgh.harvard.edu>> wrote: > > Are you using FSFAST? If you run the  preprocessing > (preproc-sess), t

Re: [Freesurfer] How to combine and divide surface-based fMRI data?

f the > > 1st run in this file. > > > > In addition, if my task design is event-related, do I need to > set the > > duration of each stimulus as 0? > > > > Thanks and best > > > > On Wed, 7 Nov 2018 at 12:59, Greve,

Re: [Freesurfer] MatrixReadTxT: could not scan value [1][1]

It is probably trying to use a default bval and bvec file, but it can't find it. If you have your bvals and bvects, try passing them explicitly to dt_recon On 11/07/2018 11:56 AM, Anwar Shatil wrote: > > External Email - Use Caution > > Hello Doug: > > > My dti_recon is getting stuck at

Re: [Freesurfer] mris_apply_reg failing for area/volume

Can you send the terminal output that includes the error? On 11/06/2018 06:36 PM, James Michael Roe wrote: > External Email - Use Caution > > Hi Bruce > > I realise that my last message made it sound as though the problem was fixed. > However, I was only confirming that the files load

Re: [Freesurfer] GLM

> > > 签名由 网易邮箱大师 <https://mail.163.com/dashi/dlpro.html?from=mail88> > 定制 > > On 11/07/2018 22:57, Greve, Douglas N.,Ph.D. > <mailto:dgr...@mgh.harvard.edu> wrote: > Use the first one. Not sure what you mean by y

Re: [Freesurfer] dcmunpack Error

You have to specify an output directory with -targ and the runs you want to unpack with -run. See the help (ie, run dcmunpack with -help) On 11/07/2018 05:38 PM, Maryam Tayebi wrote: > > External Email - Use Caution > > Hello Freesurfer Developers, > I was going to reconstruct MPRAGE

Re: [Freesurfer] T-value in QDEC or FREESURFER

On 11/03/2018 02:20 AM, Vikas Bandalli wrote: > > External Email - Use Caution > > Dear  freesurfer team. > > I am running an analysis betweene two groups Normal and Patients. > Here is an example of my particular design > diagnosis :- Normal vs Bipolar > Co-variate :- Age > Nuisance

Re: [Freesurfer] Desikian-Killiany and Destrieux atlas

I'm not sure what you mean. The atlas is distributed with FS. On 11/07/2018 05:09 PM, Miguel Ángel Rivas Fernández wrote: > > External Email - Use Caution > > > Hello Freesurfer devs, > > > Is there available any Desikian-Killiany and Destrieux atlas template > or image downloadable with

Re: [Freesurfer] mris_apply_reg failing for area/volume

gy > University of Oslo > PB 1094 Blindern > 0317 Oslo > Mobile: 958 49 437 > > > From: freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Greve, Douglas N.,Ph.D. > > Sent: 07 November 2018 19:02 > To: freesurfer@nmr.mgh.harva

Re: [Freesurfer] dcmunpack Error

09 ish. > > Thanks > > On Thu, 8 Nov 2018 at 11:55, Greve, Douglas N.,Ph.D. > mailto:dgr...@mgh.harvard.edu>> wrote: > > You have to specify an output directory with -targ and the runs > you want > to unpack with -run. See the help (ie, run dcmunpack

Re: [Freesurfer] [External] Re: Nonsensical Vertex Coordinates, please help with interpretation

__ > > From: Bruss, Joel E > > Sent: Tuesday, October 16, 2018 3:53:19 PM > > To: freesurfer@nmr.mgh.harvard.edu > > Subject: Re: [Freesurfer] [External] Re: Nonsensical Vertex Coordinates, > > please help with interpretation > > > > Attached is a screenshot showin

Re: [Freesurfer] Multivariable linear regression with binary variables

You'd have 512 groups total, which is probably way too many regardless of whether you do so manually or automatically. You need to think about how you want to model all those variables since modeling all possible interactions is not going to be possible. On 11/08/2018 12:45 PM, Worker, Amanda

Re: [Freesurfer] Functional Connectivity in FreeSurfer

Yes, see fcseedcor -help On 11/11/18 4:40 AM, Maedeh Khalilian wrote: External Email - Use Caution Dear FreeSurfer experts, I have a general question, if i have a parcellation(an annotation file e.g aparc.annot which is the output of FreeSurfer) is FreeSurfer able to calculate the

Re: [Freesurfer] [External] Re: Nonsensical Vertex Coordinates, please help with interpretation

...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <mailto:dgr...@mgh.harvard.edu> Sent: Thursday, November 8, 2018 9:26:23 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh

Re: [Freesurfer] freesurfer selxavg3-sess error

Can you include the command line and full terminal output? From what you have below, it says it is only finding one non-null condition, so double check your par files On 11/12/2018 04:58 PM, Francesca Strappini wrote: > > External Email - Use Caution > > Thank you! > I changed the event

Re: [Freesurfer] Surface failure in centos7 dev freesurfer

I just fixed it On 11/12/2018 09:35 PM, Bruce Fischl wrote: > Hi Baxter > > we are seeing this locally as well. Probably a bug introduced into > the last day or two. We will post a fix soon > > cheers > Bruce > > > On Mon, 12 Nov 2018, Baxter P. Rogers wrote: > >> External Email - Use

Re: [Freesurfer] Fwd: Manually fix FreeSurder ICV value when talairach.xfm registration is incorrect

e automatically? > > On Tue, Nov 13, 2018 at 12:13 PM Greve, Douglas N.,Ph.D. > mailto:dgr...@mgh.harvard.edu>> wrote: > > Just run > recon-all -s subject -segstats > and the new ICV should appear in the aseg.stats file > > On 11/13/2018 12:08 PM,

Re: [Freesurfer] Surface failure in centos7 dev freesurfer

.gz > SHA256 9ea8be61f2f4132770f52459a3e1c746f633727123f9f354953e93466dee165c > build-stamp.txt freesurfer-linux-centos7_x86_64-dev-20181113-8abd50c > > Thanks, > Baxter > > > Greve, Douglas N.,Ph.D. wrote: >> I just fixed it >> >> On 11/12/2018 09:35 PM, Bruce Fischl wrote: >>> Hi Baxter >&g

Re: [Freesurfer] Myelinated cortical thickness ratio map

You can use the per-voxel regressor (--pvr) option to mri_glmfit. Search through the mail archives for how to use it On 10/23/2018 06:34 AM, Damien MARIE wrote: > > External Email - Use Caution > > Hi Matt, > > Many thanks for your prompt reply, you are right. > > Any tips on how I could

Re: [Freesurfer] freesurfer selxavg3-sess error

When you ran mkanalysis-sess, did you specify two event types? You only have one non-null event in your paradigm file. On 10/28/2018 08:57 AM, Francesca Strappini wrote: > > External Email - Use Caution > > Thanks! Now it's loading correctly my event file. > However, when I run

Re: [Freesurfer] Paired Analysis Contrasts

On 10/24/2018 09:45 PM, srishti goel wrote: > > External Email - Use Caution > > Hello, > > I am trying to perform a paired analysis for a data set that has > subjects' who belong to either group1 or group2 and have data at time > point1 (tp1) and time point2 (tp2). I am following all

Re: [Freesurfer] Mapping a custom measure to the pial surface of fsaverage

rtex #n in the > pial is the closest vertex to vertex #n in the white, maybe no special > handling is needed? Right, the white and the pail use the same registratin > > Tim > >> On October 23, 2018 at 6:08 PM "Greve, Douglas N.,Ph.D." >> wrote: >

Re: [Freesurfer] How to combine and divide surface-based fMRI data?

Are you using FSFAST? If you run the  preprocessing (preproc-sess), then it will get you most of the way there. On 11/05/2018 10:16 AM, Zhi Li wrote: > > External Email - Use Caution > > Hello FreeSurfer experts, > > May I ask how can I modify the surface-based fMRI data, such as >

Re: [Freesurfer] First level modelling in task-based fMRI data

On 10/26/2018 10:53 AM, Zhi Li wrote: > > External Email - Use Caution > > Hi FreeSurfer Experts, > > Now I am trying FS-FAST in analyzing task-based fMRI data. We have two > runs for each participant. However, there were not enough events in > some runs of some participants. Hence

Re: [Freesurfer] aparcstats2table --parcs-from-file trouble

If you are using output froom mri_segstats, then you need to use asegstats2table, not aparcstats2table. It can be confusing ... On 11/01/2018 05:06 PM, Figueiro Longo, Maria Gabriela wrote: > > Hi, > > > I extracted some volumes using mri_annotation2lable --> mri_aparc2aseg > --> mri_segstats .

Re: [Freesurfer] GLM

Use the first one. Not sure what you mean by your multiple comparisons question On 11/01/2018 11:20 PM, 郑凤莲 wrote: > > External Email - Use Caution > > Hi experts, > > I am using FS 6.0 for analyzing the cortical thickness difference > between 3 groups: patient1, patient2 and control.

Re: [Freesurfer] Freeview volume measurements on newly created VOIs

mri_segstats using your VOI as the arg to --seg. Also include --excludeid 0 On 11/14/2018 06:14 PM, Kim, Jisoo,M.D. wrote: > > Hello Freesurfer developers, > > > I am trying to get volume measurements (mm^3) on VOIs (volume of > interest) that I created on Freeview. All I can do is to export the

Re: [Freesurfer] Multivariable linear regression with binary variables

From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <mailto:dgr...@mgh.harvard.edu> Sent: 08 November 2018 18:03:16 To: freesurfer@n

Re: [Freesurfer] Transformation from original dicom to skull striped output

See whether this helps. You will have to go in the opposite direction, but the idea is the same https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat On 11/12/2018 02:00 PM, Min Zhang wrote: > > External Email - Use Caution > > Dear Freesufer team: > > I have marked bounding

Re: [Freesurfer] Fwd: Manually fix FreeSurder ICV value when talairach.xfm registration is incorrect

Just run recon-all -s subject -segstats and the new ICV should appear in the aseg.stats file On 11/13/2018 12:08 PM, Gamaliz wrote: > > External Email - Use Caution > > > I have a fewT1 scans that have obvious incorrect registration > to mni_average_305. I opened tkregister2 --s subjid

Re: [Freesurfer] ?????? ?????? Recon-all run error

It looks like you might have a very big defect. Probably there is a bit of skull or cerebellum still attached. Follow the tutorial for checking for and fixing defects. On 11/14/2018 02:59 AM, 1013364183 wrote: > > ?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2External Email - Use Caution > > Dear Bruce

Re: [Freesurfer] aparc table multiple comparisons

They are not. You can compute the p-value (10^-abs(sig)), then multiply it by the number of comparisons On 11/14/2018 09:18 AM, Ralf Veit wrote: > External Email - Use Caution > > Dear list members, > > I run mri_glmfit using the aparc stats tables as input and I got a > sig.table.dat

Re: [Freesurfer] co-registration between slab of DTI image

On 11/14/2018 04:00 PM, Yixin Ma wrote: > > External Email - Use Caution > > Hi Freesurfer experts, > > I'm writing to ask about coregistration between a thin oblique coronal > slab of DTI image ( only 15 slices) and a cubic 1x1x1 voxel size > anatomical image (volume size is

Re: [Freesurfer] output values of vertices on surface into a textfile

mris_convert lh.white lh.white.asc will convert it to ascii. This file will have both xyz coordinates and neighborhood relationships, so you'll have to delete the latter. You can also load the surface into matlab with read_surf.m On 10/03/2018 11:48 AM, Sims, Sara A wrote: > > External

Re: [Freesurfer] FW: RE: error glm-fit-sim

that there is a problem with reading colortables or not? Best, Caroline Message: 2 Date: Mon, 1 Oct 2018 17:10:28 + From: "Greve, Douglas N.,Ph.D." mailto:dgr...@mgh.harvard.edu>> Subject: Re: [Freesurfer] error glm-fit-sim To: "freesurfer@nmr.mgh.harvard.edu<mailto:freesu

Re: [Freesurfer] Recon-all with/without T2 give the same stats

The aseg.stats should be the same since that does not make reference to the surfaces. The aparc stats should have been different because the thickness should have been different. Can you check whether the thickness files are different? On 10/8/18 9:39 AM, Jianzhong Chen wrote:

Re: [Freesurfer] Mri Convert Help

Sorry, there are a lot of things going on down there, it is hard to figure out what is happening. It looks like the sourcing of SetUpFreeSurfer.sh is failing is that right? Then it looks like the copy (cp) is failing. Then when you run mri_convert, it looks like another bash error. It looks

Re: [Freesurfer] Extract individual vertex thickness values from cortical parcellations

You can use matlab. read_curv.m will read in a thickness. read_annotation.m will read in the annotation. Look at the help in both for more info On 10/06/2018 11:36 AM, lindsay hanford wrote: > > External Email - Use Caution > > Hello Freesurfer Community, > > I am looking for a way to

Re: [Freesurfer] masking cortical thickness

Use the --outmask option On 10/07/2018 08:59 AM, N Saf wrote: > > External Email - Use Caution > > Dear Douglos, > > I did not understand how to use mri_label2label with the mask > option(there is srcmask options not mask alone !). I extract my labels > and as you explained I wanted to

Re: [Freesurfer] nu_correct disk i/o issues

o /tmp when it could just use ./tmp > 2) the singularity default for "sessiondir max size" is 16MB, > which includes > /tmp, is too small for the minc-tmp files > > I changed the value from 16 to 1024 and it passed the nu_correct step. > > cheers

Re: [Freesurfer] Talairach failed in monkey brain

The file passed to --reg should be a registration file. This is a text file with the transformation matrix and a few other things, not a volume file. On 10/8/18 5:28 PM, Frehiwot Woldeyes wrote: External Email - Use Caution Hello Freesurfers, I was attempting to reconstruct a monkey

Re: [Freesurfer] Recon-all with/without T2 give the same stats

, Jianzhong Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> 于2018年10月9日周二 上午10:16写道： The aseg.stats should be the same since that does not make reference to the surfaces. The aparc stats should have been different because the thickness should have been different. Can you check w

Re: [Freesurfer] analyzing and reporting parcellation results

Unless you have an a priori hypothesis about an effect in a particular ROI, then you need to correct for multiple ROIs On 10/2/18 7:25 AM, Tamir Eisenstein wrote: External Email - Use Caution Hi FS experts, When I'm analyzing regional volumes/thickness using one of the atlases ROI's

Re: [Freesurfer] Error during decompression of DICOM JPEG compressed series

What shell are you using? Try using cshell or tcshell to see if it works. On 10/2/18 4:56 AM, k3...@free.fr wrote: > External Email - Use Caution > > Hi FS team, > > I am used to run Freesurfer v6.0 on a Ubuntu 18.04 workstation and everything > runs well for most of the subjects that I

Re: [Freesurfer] Convert sig.cluster.mgh file to a binary mask in .nii format

assuming this is a surface-based analysis, then you'll need to run mri_surf2vol to convert it into a volume using fsaverage as the subject. Run it with --help to get more info On 10/2/18 5:14 AM, Carme Uribe Codesal wrote: External Email - Use Caution Dear FreeSurfer users, I am

Re: [Freesurfer] Error during decompression of DICOM JPEG compressed series

Sorry, I meant to change your default shell. That command is being run using the system() command from inside of a c-program, which undoubtedly starts your default shell. Just see if it works. On 10/02/2018 10:36 AM, k3...@free.fr wrote: > External Email - Use Caution > > I am using

Re: [Freesurfer] Error during decompression of DICOM JPEG compressed series

The command is being run from inside of a C-file using the system command, so there is no way for them to change it On 10/02/2018 01:43 PM, Dicamillo, Robert wrote: > It may be complaining about >& for redirection.  Try using 2>&1 instead. > >> On Oct 2, 2018, at 4:56 AM, k3...@free.fr

Re: [Freesurfer] Pet Surfer

Is this for an ROI-based study or a map-based study? For ROI, we use the GTM, and it PV corrects for all structures (including WM and CSF). For map-based, we use MG. MG removes WM (and CSF) entirely. In theory, it can be run in a way to keep WM and throw GM and CSF away, but that is not

Re: [Freesurfer] error glm-fit-sim (message 11)

ds (Marcel Heers) > 8. Re: hippocampal subfields (Iglesias Gonzalez, Eugenio) > 9. Re: Difference between 6.0.1 and 6.0.0 (Dicamillo, Robert) > 10. Talairach failed in monkey brain (Frehiwot Woldeyes) >11. Re: FW: RE: error glm-fit-sim (Greve, Douglas N.,Ph.D.) >

Re: [Freesurfer] Difference between 2 mgh files in surf dir (or: effects of 'mri_surf2surf --prune' without smoothing)

I think they are probably the same thing. Can you run mri_diff lh.area.fsaverage.mgh lh.area.fwhm0.fsaverage.mgh On 10/10/2018 11:12 AM, ts...@rcmd.org wrote: > External Email - Use Caution > > Dear FreeSurfer experts, > > what is the difference between the following 2 files found in a

Re: [Freesurfer] Moving VOI to FreeSurfer Space

what do you mean by FreeSurfer space? On 10/02/2018 10:11 AM, Sarosh, Cyrus wrote: > > External Email - Use Caution > > Hello FreeSurfer Experts, > > I’m trying to find the best method and command to move a hand drawn > VOI in original MRI space to FreeSurfer space. These scans have >

Re: [Freesurfer] masking cortical thickness

ted. > > BRG, > Nazanin > > > On Tue, Oct 9, 2018 at 7:27 PM Greve, Douglas N.,Ph.D. > mailto:dgr...@mgh.harvard.edu>> wrote: > > Use the --outmask option > > On 10/07/2018 08:59 AM, N Saf wrote: > > > > External Email - Us

Re: [Freesurfer] create label from cluster obtained with mri_glm-fit-sim

Which subject did you load it on? It must be fsaverage. Can you send the terminal output and command line? On 10/03/2018 11:31 PM, Ting Li wrote: > > External Email - Use Caution > > Dear Freesurfer Expert, > > I have figured out the problem is that I didn’t specify lh before the >

Re: [Freesurfer] Recon-all with/without T2 give the same stats

lh.thickness > overlaying on lh.inflated here. > > Greve, Douglas N.,Ph.D. <mailto:dgr...@mgh.harvard.edu>> 于2018年10月9日周二 下午10:22写道： > > But are the lh.thickness files the same or different? > > On 10/9/18 1:46 AM, Jianzhong Chen wrote: >> >>

Re: [Freesurfer] Pet Surfer

al Message ‐‐‐ > On Wednesday, October 10, 2018 2:17 PM, Greve, Douglas N.,Ph.D. > wrote: > >> Is this for an ROI-based study or a map-based study? For ROI, we use the >> GTM, and it PV corrects for all structures (including WM and CSF). For >> map-based, we

Re: [Freesurfer] error glm-fit-sim

What says that? What command are you running? What is the other terminal output? On 10/01/2018 04:54 AM, Caroline Beelen wrote: > > External Email - Use Caution > > Dear FS, > > I followed the group analysis page for glm analysis and it worked fine > until the final step. I’m using

Re: [Freesurfer] mri_surf2surf --mapmethod nnf not working?

Are you worried about where it says "Using surf2surf_nnfr()"? There is actually one one function that performs both kinds of mapping. In this case, it is not doing the reverse loop. You can reassure yourself by running it with nnfr and see that it prints out "Surf2Surf: Reverse Loop" (which

Re: [Freesurfer] Urgent help with preprocessing pipeline

It is hard to say. While a p-value changing from .02 to .2 seems like a lot, it does not really take much change in the values. I would look at the CVs for the individual subjects both in cross and long and see which ones are causing the change. My experience is that long is much better than

Re: [Freesurfer] Using freesurfer without intensity normalization

You'll still need to have WM at about 110 or else FS will fail. On 09/19/2018 02:48 PM, Raquib Ridwan wrote: > > External Email - Use Caution > > Hi, > > I would like to know if intensity normalization(not bias field > correction) so that white-matter is ~110 and gm is ~60 is necessary

Re: [Freesurfer] linux data and macbook

what segmentation? On 09/20/2018 12:53 PM, emre wrote: > > External Email - Use Caution > > > hi freesurfer team, > > I analyzed the data at linux, this data i can use in macbook for > segmantation? > (linux only reconall -all, other analyze in macbook) > > Is it possible without

Re: [Freesurfer] Ynt: linux data and macbook

sorry, we need way more detail On 9/20/18 11:59 PM, emre wrote: External Email - Use Caution thalamus and hippocampus Gönderen Outlook<http://aka.ms/weboutlook> Gönderen: Greve, Douglas N.,Ph.D. <mailto:dgr...@mgh.harvard.edu> adına fre

Re: [Freesurfer] if: missing file name

Not sure what is going on there. Is that really the only thing that gets printed out? Run recon-all with -debug as the first option. Capture and send us the terminal output (ie, the stuff that gets printed to the screen). Also, please make sure to include previous correspondence in your email

Re: [Freesurfer] Missing files in mri_glm

What version of FS are you using? The pcc may only be in the v6. On 09/24/2018 12:10 PM, srishti goel wrote: > > External Email - Use Caution > > Hi, > > I am running analysis to compare group difference in thickness between > two groups. I followed all the steps outlined on the wiki: >

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