Re: [Freesurfer] ERROR reading //fsaverage/label/lh.BA1_exvivo.label with recon-all.log

I'm not sure what the problem is. That recon-all.log file is for fsaverage and it says that it finished without error. Can you be more specific about the problem? On 8/21/19 10:43 PM, liuxingze1993 wrote: > > External Email - Use Caution > > Hello，Dear FreeSurfer Developers, > > I’m a do

Re: [Freesurfer] An error during data processing

It looks like there is something wrong with your dicom file because it does not have an image orientation tag (a very basic piece of information). Are you sure it is the right dicom? You can also try converting it to nifti with dcm2niix then feeding the nifti into recon-all On 8/20/19 9:59 AM,

Re: [Freesurfer] Corresponding structures to an ROI

Use bbregister instead of mri_robust_register You can then use mri_label2vol with the --seg option to map into either direction. Once they are in register, I would isolate each of your ROIs by creating a binary volume for each with mri_binarize --i yourrois.mgz --match SegId --o segid.mgz where

Re: [Freesurfer] R: syntax error near unexpected token 'newline'

You have to give it an actual path (eg, /App/freesurfer/subjeccts). When you see it means that you need to supply the something On 8/30/2019 9:42 AM, michele rizzi wrote: External Email - Use Caution Hi Bruce find attached the file. Sorry, do I have to install bash? I'm using Mojav

Re: [Freesurfer] Corresponding structures to an ROI

n code numbers? Thank you, Lily 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> Sen

Re: [Freesurfer] PETsurf kinetic modeling with MRTM

This is the time at which each frame was acquired. It is just a list of times in seconds in a text file. You will have to go to the person who collected the data On 8/30/2019 10:25 AM, Chanmi Kim wrote: External Email - Use Caution Hello, I'd like to perform MRTM2 approach in ADNI3 t

Re: [Freesurfer] PALM Analysis

Sorry, fsplam is only for surfaces. On 9/2/2019 7:46 PM, Harikumar, Amritha wrote: > Hi there, > > I am trying to run a Permutation Analysis of Linear Models (PALM) for > analyzing subcortical areas in the nucleus accumbens, caudate, and putamen. > Upon trying to run the script after reading the

Re: [Freesurfer] Compare vertexwise correlation maps

You want to see if the correlation values themselves? You can't do that (unless you have a bunch of correlation maps). You have to incorporate your question/hypothesis into the design and contrast. On 9/2/2019 11:14 AM, Matthieu VANHOUTTE wrote: > External Email - Use Caution > > Dear e

Re: [Freesurfer] mri_surf2surf without sphere.reg

Yes, just specify --surfreg white (or some other surface you do have). On 9/3/2019 9:51 AM, Caspar M. Schwiedrzik wrote: External Email - Use Caution Hi! I am having some issues projecting retinotopic mapping data from a monkey analyzed in surface space onto its surface using rtview. Th

Re: [Freesurfer] qdec contrast and data extraction

You might have done something wrong along the way. When you run the montecarlo correction, it will create a file with the thickness values in it for each cluster. the first thing to do is to load that and see if you see the expected differences. The other thing is to not go back into native spac

Re: [Freesurfer] Extracting contrast data from mri_glmfit to graph

On 9/3/19 12:05 PM, cody samth wrote: > > External Email - Use Caution > > Hello, > > I have a question regarding how to graph results that came from a > vertex wise analysis using the command mri_glmfit and mri_glmfit-sim. > > I was interested in investigating an interaction effect betw

Re: [Freesurfer] make_average_subject error

Is BrainaverageN72 in the subjects list? On 9/3/19 12:39 PM, Maxime Perron wrote: > > External Email - Use Caution > > ​Dear Freesurfer Experts, > > > I have the following issue when running the make_average_subject command ( > > make_average_subject --subjects (Subjid) --out BrainaverageN

Re: [Freesurfer] Clusterwise correction for multiple comparisons

If it is only one space, then you can just leave off --3spaces On 9/3/19 1:48 PM, Gwang-Won Kim wrote: > > External Email - Use Caution > > Hi there, > To perform a cluster-wise correction for multiple comparisons, I ran > monte carlo simulation as follows: mri_glmfit-sim --glmdir g1v2.wl

Re: [Freesurfer] Compare vertexwise correlation maps

; Best, > Matthieu > >> Le 3 sept. 2019 à 17:00, Greve, Douglas N.,Ph.D. a >> écrit : >> >> You want to see if the correlation values themselves? You can't do that >> (unless you have a bunch of correlation maps). You have to incorporate >> your quest

Re: [Freesurfer] PALM Analysis

uot;Re: Contents of Freesurfer digest..." >> >> >> Today's Topics: >> >>1. OHBM International Mentoring Programme Sign-up {Disarmed} >> (Meena M. Makary) >>2. PALM Analysis

Re: [Freesurfer] paired t-test for pet surface analysis

If you are going to do a paired test, then each subject can only have 2 time points On 9/4/19 11:58 AM, miracle ozzoude wrote: > > External Email - Use Caution > > Hello Freesurfer, > > I am trying to run a surface based paired ttest for pet. I started by > running mri_vol2surf for each

Re: [Freesurfer] Question about how to build .gca files from non-human atlas and images

Sorry, I think this is beyond our ability to support. On 9/4/19 4:44 AM, arsene ella wrote: > > External Email - Use Caution > > /Dear //Freesurfer experts,/ > > /I’ve built an atlas of structures of a non-human average brain and now //I > would like to build //its//.gca files from scratc

Re: [Freesurfer] make_average_subject error

quot; > "Freesurfer_S144" "Freesurfer_S145" "Freesurfer_S146" "Freesurfer_S147" > "Freesurfer_S148" "Freesurfer_S150" "Freesurfer_S151" "Freesurfer_S152" > "Freesurfer_S153" "Freesurfer_S

Re: [Freesurfer] Scale Option for mris_convert

That scales the coordinates and will have no effect on the file size. Try mris_decimate instead. Note that the version 6 mris_decimate is not deterministic. I've put a deterministic one here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mris_decimate On 9/4/19 2:49 PM, roc...@netzero.net wrot

Re: [Freesurfer] Siemens Enhanced DICOM

Try using dcm2niix (not part of FreeSurfer) to convert to nifti On 9/4/19 3:44 PM, Funk, Quentin wrote: > > External Email - Use Caution > > Hey all- > > Freesurfer's recon-all fails if I try to give it a dicom from the new > Siemens Enhanced format. Are there any workarounds that don't i

Re: [Freesurfer] Problem with lGI

Don't know. Looks like it is some kind of internal matlab error. Did you recently change versions? btw We are no longer supporting lGI at this time. On 9/3/2019 12:11 PM, Avi Gharehgazlou wrote: External Email - Use Caution Hi, I have ran the lGI flag many times in the past. However, n

Re: [Freesurfer] qdec contrast and data extraction

t; > Basically, what is the correct way to extract values from these significant > clusters? > > Many thanks, > Omar > > Date: Tue, 3 Sep 2019 15:15:02 + > From: "Greve, Douglas N.,Ph.D." > Subject: Re: [Freesurfer] qdec contrast and data extrac

Re: [Freesurfer] issue with lesions

You can get the volume from the aseg.stats file. Unfortunately, we do not separate the lesions into left and right. You could do something like mri_binarize --i aseg.mgz --match 77 --o wmlesions.mgz mri_volcluster --i wmlesions.mgz --sum lesions.sum.dat --thmin 0.5 --regheader subject This will o

Re: [Freesurfer] make_average_subject error

9, at 6:10 PM, Greve, Douglas N.,Ph.D. <mailto:dgr...@mgh.harvard.edu> wrote: Can you send the full text of the terminal output? On 9/4/19 10:44 AM, Maxime Perron wrote: External Email - Use Caution Hi Greve, The exact script is the following : setenv SUBJECTS_DIR

Re: [Freesurfer] ERROR reading //fsaverage/label/lh.BA1_exvivo.label with recon-all.log

Does this file exist /media/dell/AA32E66632E6374B/Data_prac/220liujiayue/20181217/fsaverage/label/lh.BA1_exvivo.label and do you have read permissions to it? On 9/5/2019 5:39 AM, liuxingze1993 wrote: External Email - Use Caution Hello， Dear FreeSurfer Developers, Hi, I'm attempting to f

Re: [Freesurfer] qcache after running recon-all post correction processing

You can just run recon-all again with only the -qcache flag (this is actually how it is intended to be run) On 9/5/2019 2:52 PM, Swanson,Clayton wrote: External Email - Use Caution Hi FreeSurfer folks, I searched through the archives and was unable to find the answer I was looking for

Re: [Freesurfer] mri_glmfit error

Did you see the part where it says "If you seek help with this problem, make sure to send:"? On 9/5/2019 11:00 PM, Gwang-Won Kim wrote: External Email - Use Caution Hi there, I tried to analysed "mri_glmfit --glmdir g1v7.wls --y ces.nii.gz --wls cesvar.nii.gz --C Main.mtx --C PDI.mtx

Re: [Freesurfer] Morphological Features, Description & References

For cortical volume we compute vertex-wise volume based on dividing each obliquely truncated trilateral pyramid into three tetrahedra. Based on Anderson M. Winkler's srf2vol matlab script. On 9/6/2019 10:22 AM, Bruce Fischl wrote: Hi Philipp I'll leave the volume question to Doug. The curv

Re: [Freesurfer] Question about how to build .gca files from non-human atlas and images

Dear Douglas, I know that you are very busy by a lot of other people to support but I don't understand your answer about my questions and disappointed by it... Did I say or do something wrong? Regards, Arsene Le jeu. 5 sept. 2019 à 00:12, Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.ed

Re: [Freesurfer] Command line tksurfer: use of the color scale "Color Wheel"

Hi Caspar, sorry for the delay. I have not used the retinotoy stream in a long, long time so I don't know off the top of my head. I'll have to look into it. tksurfer (from rtview) does have a way to display using the color wheel, but I don't remember how to do it. Ruopeng, can freeview display

Re: [Freesurfer] Extracting contrast data from mri_glmfit to graph

Right, the ocn.dat files have data that is uncorrected in that sense and might need to nuisance factors removed before plotting. There is a design matrix in there (Xg.dat). You can load that into matlab along with the ocn.dat, compute beta = inv(X'*X)*(X'*ocn) to get the betas. You can then comp

Re: [Freesurfer] fspalm error

I think palm itself requires mgh or mgz files. I can't remember why we don't convert it. You can run mri_glmfit with --mgz or --mgh (or just without --nii.gz) and it should work. On 9/9/2019 9:24 AM, Barbour, Tracy,M.D. wrote: Hello Freesurfer community! I am trying to run fspalm on surface ba

Re: [Freesurfer] freesurfer 6.0 hires fix

You have to rerun from the beginning. (sorry) On 9/9/19 3:12 PM, Aaron Tanenbaum wrote: > > External Email - Use Caution > > I noticed that you guys released a fix to improve the -hires option.  > I have been processing some of our data using the hires flag. if i use > this fix do i need

Re: [Freesurfer] Extracting contrast data from mri_glmfit to graph

olumns from the Xg.dat file > yhat = X2*beta2 ' saved these values and plotted them against my > variable of interest > > > On Mon, Sep 9, 2019 at 10:37 AM Greve, Douglas N.,Ph.D. > mailto:dgr...@mgh.harvard.edu>> wrote: > > Right, the ocn.dat files have data

Re: [Freesurfer] Convert nifti atlas into .annot file

Run recon-all on the anatomical templates, then use mri_vol2surf (wiht --projfrac 0.5) to sample the segmentations onto the surface, then use mris_seg2annot to convert to annotation On 9/9/19 6:10 PM, Dev vasu wrote: > > External Email - Use Caution > > > Dear all, > > How can i create .

Re: [Freesurfer] Command failed in QDEC

It might be that the design matrix is ill-conditioned. Did it print anything to the terminal? Also, we are not really supporting qdec anymore, so you can try using the command-line stream (ie, mris_preproc, mri_surf2surf, mri_glmfit, mri_glmfit-sim) On 9/10/19 2:36 AM, James Karantonis wrote: >

Re: [Freesurfer] Command line tksurfer: use of the color scale "Color Wheel" {Disarmed}

> > External Email - Use Caution > > Hi Doug and Ruopeng, > it would be amazing if you could dig out the information on how to > display the color wheel. > Looking forward to what you find! > Caspar > > > Am Fr., 6. Sept. 2019

Re: [Freesurfer] Opseq2 question

If you are going to assume a shape to the hemodynamic response, then I don't think it makes much difference. It will make a difference if you are going to use an FIR. On 9/9/19 10:49 AM, Nasiriavanaki, Zahra wrote: > Hi Freesurfer experts > > I have a question about designing an event related ta

Re: [Freesurfer] Fw: question on GLM

y results ok? > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Greve, Douglas > N.,Ph.D. > *Sent:* Friday, September 6, 2019 12:46 PM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] Fw: question on

Re: [Freesurfer] Opseq2 question

Hospital > > 149 13th Street, 149-2615 > > Charlestown, MA, USA, 02129 > > > > ------------ > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Greve, Douglas > N.,Ph.D. > *Sent:* Tuesday, September 10, 2019 11:24 AM > *To:*

Re: [Freesurfer] Custom Segmentation of the Cortex usable with mri_compute_volume_fractions

Do you mean you want to separate the volume fractions between two adjacent segmentations rather than just all of cortex? On 9/10/19 10:04 AM, Pfannmoeller, Joerg Peter wrote: > Hello, > > I would like to generate a custom segmentation of the cortex. That > segmentation should be restricted to a

Re: [Freesurfer] -qcache recon-all exciting with error

This usually happens when a subject was run all the way through recon-all once, then again but only part of the way (eg, after editing). Check those subjects to see what happened. On 9/10/2019 5:34 PM, Swanson,Clayton wrote: External Email - Use Caution Hello FreeSurfer Developers, I a

Re: [Freesurfer] multiple comparisons correction for brain-behaviour correlations

I think you could get the p-valueus for the clusters and do FDR on those (or maybe the most significant of more than one cluster in a given comparison) On 9/11/19 9:26 AM, Annelies Vant Westeinde wrote: External Email - Use Caution Dear members, I have run several analyses in which we

Re: [Freesurfer] timewindow parameter in mkanalysis-sess

relevant, but it seems weird. Maybe it was already addressed in version 6. Caspar Am Di., 13. Aug. 2019 um 22:51 Uhr schrieb Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>>: That is in response to a 60 sec stimulus. The time window is the time needed to account for a very brief st

Re: [Freesurfer] Downsampling from fsaverage to fsaverage6

This is a bug. I've fixed it in our development version. You can download an update from here https://gate.nmr.mgh.harvard.edu/safelinks/greve/mri_surf2surf On 9/13/19 8:00 AM, Matthieu VANHOUTTE wrote: External Email - Use Caution Dear FS's experts, I am trying to downsample some surfac

Re: [Freesurfer] Questions about labels and tkmedit

Not that I know of, it is pretty limited. On 9/13/19 11:13 AM, Zeng,Victor (BIDMC - Psychiatry) wrote: Hi all, ​ I know tkmedit has been deprecated, but we're thinking about using it just for quality check purposes since we found that it is less resource intensive. We're trying to load multip

Re: [Freesurfer] Extract ThickAvg ThickStd from rh/lh.aparc.stats of a specific structure for group of subjects

You can use a PARCSFILE. Run aparcstats2table with --help to get more info On 9/14/19 3:30 PM, vin rasa wrote: External Email - Use Caution Dear Freesurfer experts, Is there a shortcut to extract mean thickness(ThickAvg) and std (ThickStd) from rh/lh.aparc.stats for let's say 4 structu

Re: [Freesurfer] mkcontrast-sess question

Are you trying to do a parametric analysis? See https://surfer.nmr.mgh.harvard.edu/fswiki/FsFastParametricModulation On 9/13/19 11:08 AM, Nasiriavanaki, Zahra wrote: Dear Freesurfer experts Hi I have a question about weighting different contrasts using mkcontrast-sess commmand. I have single s

Re: [Freesurfer] Recon-all on a cluster error

Does it run properly off the cluster for this data set? On 9/17/19 1:45 PM, Lauricella, Michael wrote: > > External Email - Use Caution > > Dear Freesurfer Experts, > > I have a an error when running recon-all on a computing cluster. I’ve > checked the environment and so have some of my m

Re: [Freesurfer] PET input file for mri_gtmpvc

I would use unstripped, but it probably won't make much difference. Just make sure that the registration is good. On 9/17/19 1:48 PM, Jane Tseng wrote: > > External Email - Use Caution > > Dear Freesurfer experts, > > I was wondering if there is any recommendation on the PET input file >

Re: [Freesurfer] mri_convert for Philips dicoms

Try dcm2niix (not part of FS, you'll have to download and install) On 9/17/19 3:10 PM, Mun, Anna wrote: > Dear FreeSurfer team, > > I am working with data sent to us from other research site. They use > Philips scanner and I can not run mri_convert on the dicoms. Is there > other way to mri_conv

Re: [Freesurfer] Recon-all on a cluster error

gt; > Best, > Michael > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > On Behalf Of Greve, Douglas N.,Ph.D. > Sent: Tuesday, September 17, 2019 10:50 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Recon-all on a cluste

Re: [Freesurfer] qdec contrast and data extraction

t;// > >/Which specific file should I load? I see cluster.mgh, > cluster.summary, sign.ocn.annot, sig.ocn.mgh, sig.vertex.mgh, and > pdf.dat./ > >// > >/How can I extract the values from fsaverage space?/ > >// > >/Basically, what is the correct

Re: [Freesurfer] Cortical thickness (spc) extraction

You can run corrections for multiple comparisons (mri_glmfit-sim) to get clusters of significant effects, then compute the mean over those clusters. On 9/19/19 8:08 AM, AKUDJEDU, THEOPHILUS wrote: > > External Email - Use Caution > > > Dear FreeSurfer, > > I used QDEC for the longitudinal

Re: [Freesurfer] issue with lesions

the > recommended way to fix a bad segmentation due to cerebellum lesions? > Control points, white matter edits, or something else? > Sam > > On Fri, Sep 6, 2019 at 4:28 PM Greve, Douglas N.,Ph.D. > mailto:dgr...@mgh.harvard.edu>> wrote: > > You can get the volum

Re: [Freesurfer] Obtaining MNI Coordinates for HCP annotations

What space are they in? Typically, I tell people to run recon-all on the mni152 volume, then map labels into that subject, then compute coords On 9/13/19 3:00 PM, Dev vasu wrote: > > External Email - Use Caution > > Dear all, > > I would like to obtain MNI coordinates for HCP annotations

Re: [Freesurfer] Recon-all on a cluster error

ob D who can help > debug this problem if it persists. > doug > > > On 9/17/19 1:57 PM, Lauricella, Michael wrote: >> External Email - Use Caution >> >> Hi Douglas, >> >> Yes it does fine. On the cluster, this same error happens for all subjects. >> >>

Re: [Freesurfer] Default GCA atlas FreeSurfer 6?

here it is $FREESURFER_HOME/average/RB_all_2016-05-10.vc700.gca This is a "GCA" file (gaussian classifier array), not a simple image. You can get an image out of it by running mri_convert on it On 9/20/2019 11:56 AM, Brehler, Michael wrote: External Email - Use Caution Hello FreeSurfer

Re: [Freesurfer] GLM analysis question

On 9/23/2019 10:54 AM, Ferraro, Pilar wrote: > External Email - Use Caution > > To the kind attention of the FreeSurfer team, > > I have some questions concerning a GLM analysis I’m running and any help > would be greatly appreciated! > I’m interested in identifying cortical regions whe

Re: [Freesurfer] mri_glmfit: don't display "positive"

In freeview, you can select with sign you want to view (I think it is called "truncation"). Is that what you mean? On 9/20/2019 2:48 PM, Rockers, Elijah D. wrote: External Email - Use Caution Hello, with Qdec, there was an option to "remove" positive (or negative) results from the d

Re: [Freesurfer] issue with lesions

s not align well with orig.mgz... Best regards, Sam On Thu, Sep 19, 2019 at 4:54 PM Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> wrote: There is not an easy way to do this. FS expects an intact whole brain, and it tries to fit such into every brain, ie, it is trying to force a whole

Re: [Freesurfer] Unable to access previous email archives

I did not have any problems. Were you on this link? https://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/ On 9/25/19 10:10 AM, Mageshwar Selvakumar wrote: > > External Email - Use Caution > > Dear Freesurfer community, > > I have not been able to access the mail archives this week.

Re: [Freesurfer] issue with lesions

above. > Do you have an idea what I might be doing wrong? > > Best regards, > Sam > > On Mon, Sep 23, 2019 at 8:18 PM Greve, Douglas N.,Ph.D. > mailto:dgr...@mgh.harvard.edu>> wrote: > > mri_coreg should have printed out tkregisterfv command. Try > running t

Re: [Freesurfer] Hippocampal Subfields Atlas

Are you using fsfast? On 9/25/19 7:00 AM, ZZY wrote: > > ?0?2?0?2?0?2?0?2?0?2?0?2?0?2?0?2External Email - Use Caution > > Dear ?0?2Doug?? > > ?0?2 ?0?2 ?0?2I have a group of multimode MRI data, including functional MRI, > T1WI and diffusion MRI. We want to analyze the functional and > structual

Re: [Freesurfer] Freesurfer vs. CAT12

Hi Omar, we have played around with CAT12 a little bit and are finding systematic differences (eg, CAT thickness is thicker than FS). In the one study we tried, the group analysis was quite different. We have not had time to really dig into it yet. best doug On 9/20/19 3:14 PM, Maximo, Jose Oma

Re: [Freesurfer] Corpus Callosum area

We don't output or have tools to compute it. I can tell you how you can get a number for it, but it would not be with a validated method. Let me know. On 9/24/2019 5:37 AM, Fernanda Hansen P. de Moraes wrote: External Email - Use Caution Dear Freesurfer experts, how can I extract the c

Re: [Freesurfer] Question about using tkregisterfv to check registration

Can you run tkregisterfv --debug --mov pet.nii.gz --targ T1.nii --reg pet_T1.reg.lta and send the terminal output? On 10/2/2019 3:58 PM, Vicky Yang wrote: External Email - Use Caution Dear Freesurfer experts, I used mri_coreg to register my pet data to T1 like below: mri_core

Re: [Freesurfer] Freesurfer three groups: group A vs C power.

The DOF is determined only from the design matrix as DOF = #RowsX - #ColsX So, it would be 9 regressors, not 6 On 9/26/2019 12:31 PM, cody samth wrote: External Email - Use Caution Hi I have a question regarding how freesurfer calculates the degrees of freedom when you have three groups

Re: [Freesurfer] selxavg3-sess

It is having some problems unzipping a nifti file. Does it work on other runs/sessions/subjects? If so, then there might be something wrong with that file. Alternative, check /var/volders/v3 to see if the disk is filling up. On 10/1/2019 1:43 PM, Sanati Monfared, Shamsi wrote: External

Re: [Freesurfer] Question on Z-scoring

That looks correct to me On 10/4/2019 5:39 PM, Nillo, Ryan Michael R wrote: Hello FreeSurfer users/devs, I have a question on z-scoring. I would like to produce z-scored volume maps for each subject in my study. Is my process correct? 1) mri_surf2surf —srcsubject $sub —trgsubject $sub —sval $su

Re: [Freesurfer] ERROR gtmseg

That is kind of weird. It says it has found a segmentation with number 229, but we don't have that code in our system. Can you find the 229 voxels in the aparc+aseg.mgz? On 10/4/2019 6:28 PM, Marina Fernández wrote: External Email - Use Caution Dear experts, The following error occurs

Re: [Freesurfer] Segmentation faule recon-all

Did you check the talairach transform? See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/Talairach_freeview On 10/4/2019 1:37 PM, Backhausen, Lea wrote: External Email - Use Caution Dear FreeSurfer experts, when running the recon -all –all command (I included the -3T flag) with

Re: [Freesurfer] What's the difference between FSFAST and SPM in the 1-st level GLM?

It is hard to say exactly what the difference is, but in the command below, you set the high-pass cutoff to be 128 Hz meaning that it will try to filter out everything below 128Hz, which is undoubtedly where your signal is. Probably you meant to use something like -hcp .01 or so On 9/27/2019 11

Re: [Freesurfer] mri_surf2vol -lost cluster

You can ask it to sample the maximum along the surface normal over a certain distance. Use --projdist-max. Run mri_vol2surf --help for more info On 9/27/2019 2:04 PM, Albrecht, Daniel S. wrote: Hello everyone, I've been using mri_vol2surf to move some activation data in MNI space to the fsavera

Re: [Freesurfer] Corpus Callosum area

às 21:10, Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> escreveu: We don't output or have tools to compute it. I can tell you how you can get a number for it, but it would not be with a validated method. Let me know. On 9/24/2019 5:37 AM, Fernanda Hansen P. de Moraes wrote:

Re: [Freesurfer] mask of premotor cortex and primary cortex

Try using 1024 (precentral) and 1022 (postcentral) with the aparc On 10/3/2019 3:11 AM, sang ho shin wrote: External Email - Use Caution Dear Freesurfer Developers, I have analyzed connectivity between striatum and different brain cortex with diffusion weighted MRI. I completed recon-a

Re: [Freesurfer] Main effect of sex for total surface area, but not for summed vertex-wise surface area

How did you map the area to fsaverage? If you don't do it properly, you can get some funny results because area has to be jacobian corrected. On 10/3/2019 8:03 AM, Linn Christin Bonaventure Norbom wrote: External Email - Use Caution Hello all Freesurfer experts! Through my analysis

Re: [Freesurfer] Question about settig up FS-FAST file hierarchy

The easiest way is to use dcmunpack. See http://surfer.nmr.mgh.harvard.edu/fswiki/FsFastFunctionalConnectivityWalkthrough On 10/5/2019 1:55 PM, Hossein Sanjari Moghaddam wrote: External Email - Use Caution Dear officer, Greetings. We are working on a set of resting-state fMRI data using

Re: [Freesurfer] Confidence interval for Cohen's d from gamma/rstd

You want the 95% CI for Cohen's d itself? I don't know how to do that. If you just want it for the contrast (gamma), then I would just use the formula for a gaussian with mean gamma and stddev sqrt(gammavar) On 10/5/2019 10:43 AM, Caspar M. Schwiedrzik wrote: External Email - Use Cauti

Re: [Freesurfer] Error in glmfit-sim cache

It looks like it might be a locale problem as it thinks that you are inputing "4,0" with a decimal comma instead of a decimal point. Try using "4.0" instead of "4" On 10/5/2019 5:21 PM, Renew Andrade wrote: > External Email - Use Caution > > Dear FreeSurfer experts: > I have an issue wh

Re: [Freesurfer] Comparing effects between voxels in a FFX GLM

I'm not sure what you are trying to do. You want to compare the signal in one voxel vs another voxel in the same map? On 10/7/2019 10:32 AM, Caspar M. Schwiedrzik wrote: External Email - Use Caution Hi Doug, I would like to test whether an effect that I observed in a given voxel is lar

Re: [Freesurfer] question on mris_calc - re-submitting

Yes, you can also just use fscalc image1.mgh sub image2.mgh div image2.mgh -o final.mgh On 10/7/2019 10:40 AM, Barletta, Valeria wrote: From: Barletta, Valeria Sent: Friday, September 27, 2019 12:30 PM To: freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] Vertex by Vertex Analysis

Run mris_preproc with the usual arguments but specify --meas w-g.pct.mgh Then run the rest of the group analysis as if it were a surface file. On 10/4/2019 6:44 PM, WON JONG CHWA wrote: External Email - Use Caution Hello, I would like to perform a group difference analysis with gray-whi

Re: [Freesurfer] question about aparcstats2table

You can create a file called SUBJECTSFILE with all your subjects in it, then run aparcstats2table with the following option --subjectsfile=SUBJECTSFILE On 10/3/2019 11:07 AM, chen wrote: External Email - Use Caution Hi FreeSurfer experts, I want to converts a cortical stats file into a

Re: [Freesurfer] Brodmann area parcellation

You can to run the full recon-all on a given subject's data, and it will create the broadmann areas On 10/5/2019 1:31 AM, sang ho shin wrote: External Email - Use Caution Dear Freesurfer Developers, I am trying to get the seed mask of premotor and motor cortex. Because I can't get it

Re: [Freesurfer] Question about using tkregisterfv to check registration

there any way to improve the registration? Thanks again for your time! Regards, Vicky On Wed, Oct 2, 2019 at 5:36 PM Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> wrote: Can you run tkregisterfv --debug --mov pet.nii.gz --targ T1.nii --reg pet_T1.reg.lta and send the terminal outpu

Re: [Freesurfer] Label created in the symmetric space

Let's backup a moment. Can you send the y.ocn.dat file that has problematic values? On 10/4/2019 4:58 AM, Jose Graterol wrote: External Email - Use Caution Dear Freesurfer Experts, I would appreciate your help. I will explain first what I have done and where my problem is. I want to

Re: [Freesurfer] Comparing effects between voxels in a FFX GLM {Disarmed}

Mo., 7. Okt. 2019 um 17:15 Uhr schrieb Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>>: I'm not sure what you are trying to do. You want to compare the signal in one voxel vs another voxel in the same map? On 10/7/2019 10:32 AM, Caspar M. Schwiedrzik wrote: External

Re: [Freesurfer] ERROR gtmseg

Sorry, can you include the previous correspondence so that I know the context? On 10/7/2019 11:45 AM, Marina Fernández wrote: External Email - Use Caution Dear Douglas, Thank you for the replay. I think so, I can't find the code 229 in any subject. I can't see anything strange in the

Re: [Freesurfer] Brodmann area parcellation

0 16777216 0.00 mri_binarize done [https://mailfoogae.appspot.com/t?sender=aaGFwcHlzYXJhbTIwQGdtYWlsLmNvbQ%3D%3D&type=zerocontent&guid=6b3eb091-0795-4417-89b6-d8bd71bc969b]ᐧ 2019년 10월 7일 (월) 오후 4:20, Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>&

Re: [Freesurfer] Label created in the symmetric space

file. On 10/7/2019 11:53 AM, Jose Graterol wrote: External Email - Use Caution Hi Douglas, thanks for you answer. I have attached the file to the email. On Mon, Oct 7, 2019 at 5:24 PM Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> wrote: Let's backup a moment. Can y

Re: [Freesurfer] ERROR gtmseg

We'll have to figure out where those 229s are coming from. Try this mri_binarize --i aseg.presurf.mgz --match 229 --o bin229.mgz It should print out whether there were any voxels that matched. If so, you can load bin229.mgz with the norm.mgz and the aseg.presurf.mgz and see where they are. If the

Re: [Freesurfer] Question about using tkregisterfv to check registration

stand why it is going awry. And suggestions? Thanks, Vicky On Mon, Oct 7, 2019 at 11:21 AM Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> wrote: You can manually change the registration in tkregisterfv. But we rarely see this happen and I'm wondering if it might be some other

Re: [Freesurfer] FreeSurfer freezing during processing.

We don't have a lot of experience running recon-all on windows-ubuntu, but I do know that people do so successfully. It does seem weird that mri_em_register is taking over an hour. Do you have a lot of other things running at the same time? If so, try running with just recon-all On 10/3/2019 9:

Re: [Freesurfer] ERROR gtmseg

., 7 oct. 2019 a las 23:19, Greve, Douglas N.,Ph.D. (mailto:dgr...@mgh.harvard.edu>>) escribió: We'll have to figure out where those 229s are coming from. Try this mri_binarize --i aseg.presurf.mgz --match 229 --o bin229.mgz It should print out whether there were any voxels that matched.

Re: [Freesurfer] Label created in the symmetric space

"glmdir.jg.allsubjects.tar.gz". I had to log in as anonymous and not with my email, otherwise it would throw an error (503 Login with USER first. Login failed.). The mgh file is inside the gz file too. Thanks again for your time and help. On Mon, Oct 7, 2019 at 7:06 PM Greve, Douglas N.,Ph.D.

Re: [Freesurfer] Label created in the symmetric space

.lh.lesion-healthy.thickness.sm10.mgh >  --glmdir glmdir.allsubjects.lh.lesion-healthy.thickness.sm10 > --cwpvalthresh 0.05 --cache 4 neg > > > Hopefully this helps. > > > > > On Tue, Oct 8, 2019 at 4:45 PM Greve, Douglas N.,Ph.D. > mailto:dgr...@mgh.harvard.edu>>

Re: [Freesurfer] Read out N from mri_glmfit outputs?

look in the glmdir/dof.dat file On 10/8/19 11:00 AM, Caspar M. Schwiedrzik wrote: > > External Email - Use Caution > > Hi! > Is there a way to read out the N of a fixed effects analysis performed > with mri_glmfit? > If not, is it safe to assume that it is (number of volumes*number of >

Re: [Freesurfer] Label created in the symmetric space

wrote: > > External Email - Use Caution > > Aha, yes. That is what I want. The original thickness values. > > Greve, Douglas N.,Ph.D. <mailto:dgr...@mgh.harvard.edu>> schrieb am Di., 8. Okt. 2019, 17:36: > > That all looks fine, I'm just not sure what problem you want

Re: [Freesurfer] Main effect of sex for total surface area, but not for summed vertex-wise surface area

ing mri_preproc on area,​ is that correct? > > Thanks so much for helping me out with this, I really appreciate it! > Linn > > > ------------ > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > on behalf o

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