Re: [Freesurfer] Freesurfer 6 current state of submillimeter processing

Use the patch On 10/10/2019 11:07 AM, Daniel Westfall wrote: External Email - Use Caution Hi Everyone, I just wanted to double check the current state of processing T3 submillimeter data with Freesurfer 6. We have two studies: one with 0.9 mm isotropic and the other with 0.8 mm isotro

Re: [Freesurfer] Assign different number in FreeSurferColorLUT

The easiest thing is probably to set the output value when running mri_binarize with the --binval option. Eg, left amygdala would be --binval 18 On 10/10/2019 6:09 PM, Gwang-Won Kim wrote: External Email - Use Caution Hi there, I made the 3 ROIs (Thalamus, amygdala, putamen) using "mri

Re: [Freesurfer] fsaverage label into functional space

This appears to be a bug in mri_label2vol when you specify a surface. Instead, you can create a volume in the conformed space, and then use mri_label2vol with that volume as the --seg input. BTW, you should use mri_label2label to map from fsaverage into the individual subject space, then do the

Re: [Freesurfer] imperfect segmentation in the occipital lobe in epilepsy patient

I think that the wm edits should have worked. Can you load the rh.orig.nofix and rh.orig to see if they encompass your edits? If not, then maybe your did not re-run it properly. On 10/8/2019 12:22 PM, Xiaoqian Yan wrote: External Email - Use Caution Dear Freesurfer experts, I am tryin

Re: [Freesurfer] brain mask without CSF ...

You will have to do it manually. You can create a binary CSF mask from the aseg.mgz using mri_binarize. Don't use 702 and 703 -- those refer to "FSL-FAST" not "FS-FAST". Try using the --vcsf flag to mri_binarize (ventricular csf). Then use mri_label2vol to map it into the functional space. Once

Re: [Freesurfer] local Gyrification Index

Sorry, the person who used to support the gyrification software has left. You're kind of on your own unfortunately. On 10/11/2019 6:04 AM, LOSKE, PHILIPP (PGR) wrote: External Email - Use Caution Hello FreeSurfer Team, I am trying to compute the local Gyrification index on my subjects

Re: [Freesurfer] Freesurfer using dof9 with preproc-sess

This is a bug. I think I have fixed it. Can you download these files https://gate.nmr.mgh.harvard.edu/safelinks/greve/preproc-sess https://gate.nmr.mgh.harvard.edu/safelinks/greve/rawfunc2surf-sess https://gate.nmr.mgh.harvard.edu/safelinks/greve/rawfunc2tal-sess Copy them to $FREESURFER_HOME/fsf

Re: [Freesurfer] using dof9 or dof12 in preproc-sess

just posted solution to the freesurfer list. Are you running your analysis local to the martinos center? On 10/11/2019 11:02 AM, Droppa, Kyle Salmon wrote: Hello, I posted this earlier and wasn't able to get a response. I am using freesurfer version 6 and I am having an issue with changing the

Re: [Freesurfer] Freesurfer using dof9 with preproc-sess

You will also need https://gate.nmr.mgh.harvard.edu/safelinks/greve/register-sess https://gate.nmr.mgh.harvard.edu/safelinks/greve/mkbrainmask-sess On 10/11/2019 11:12 AM, Douglas N. Greve wrote: This is a bug. I think I have fixed it. Can you download these files https://gate.nmr.mgh.harvard.e

Re: [Freesurfer] ERROR gtmseg

Can you upload one of your problematic subjects? Follow these instructions From the linux command line, Create the file you want to upload, eg, cd $SUBJECTS_DIR tar cvfz subject.tar.gz ./subject Now log into our anonymous FTP site: ftp surfer.nmr.mgh.harvard.edu It will ask you for a user name: us

Re: [Freesurfer] Learning dti processing tutorial

What is the input file that you are supplying? Often this happens when the input it a multi-echo MPRAGE. If so, you can run mri_concat multi-echo-mprage.mgz --rms --o mprage.mgz then use mprage.mgz as the input to recon-all On 10/12/2019 4:48 PM, Renew Andrade wrote: > External Email - U

Re: [Freesurfer] FS-FAST: cluster size from 1st level analysis

Sorry for the delay ... First, run selxavg3-sess with -fwhm ( you might need to delete the bold/analysis folder to get it to re-run). cd session/bold/analyis There will be a filed called fwhm.dat. Look in that. Depending upon how much you smoothed it might be something like 10.395. This is the

Re: [Freesurfer] FS-FAST: cluster size from 1st level analysis

--csd is used? Thanks, Keri On Tue, Oct 15, 2019 at 4:17 AM Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> wrote: Sorry for the delay ... First, run selxavg3-sess with -fwhm ( you might need to delete the bold/analysis folder to get it to re-run). cd session/bold/analyis There w

Re: [Freesurfer] recon-all at native resolution

better to use a patch I created for the HCP, see https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp/readme On 10/15/19 12:13 PM, Alexopoulos, Dimitrios wrote: > > External Email - Use Caution > > We have data acquired at 0.8mm isotropic and would like to maintain > th

Re: [Freesurfer] FSGD file formatting for Xhemi

What are you trying to test? Usually you don't have lh and rh in the same glm On 10/17/19 7:09 AM, Jose Graterol wrote: External Email - Use Caution Dear Freesurfer Community, I have a question regarding the formatting of the FSGD file while doing an analysis with Xhemi. First the --y

Re: [Freesurfer] aseg.stats format FreeSurfer 5 versus 6

They are just different names On 10/17/19 11:52 AM, Tim Schäfer wrote: > External Email - Use Caution > > Dear fs experts, > > I'm parsing aseg.stats files for subjects to extract global brain measures > and noticed that at least 2 names changed from FreeSurfer 5.1 versus > FreeSurfer 6

Re: [Freesurfer] ERROR gtmseg

Oh, yes, sorry. The problem was that you are using FS 5.1 segmentations and things have changed since then in a way that makes it incompatable with gtmseg. One possibility is to run gtmseg with --ctab $FRESURFER_HOME_51/FreeSurferColorLUT.txt If that does not work, you may need to reanalyze your

Re: [Freesurfer] QDEC cluster output

Hi Lara, sorry, we don't really support qdec anymore for the very reason that we can't get into the code easily and answer these questions. Can you use the command-line stream? doug On 10/17/19 6:17 PM, Lara Foland-Ross wrote: External Email - Use Caution Hi Freesurfer experts, I’m ru

Re: [Freesurfer] Group effect Contrast for 6 groups

Yes, that is correct. It is testing the null hypothesis A=B=C=D=E=F. That hypothesis will be rejected if A is different from B-F, which is what you are testing. The other contrasts are redundant (and would cause an error if you added them to the contrast matrix)z On 10/16/19 12:03 PM, cody samt

Re: [Freesurfer] covariate with repeated anova

I'm not sure how to do this in the RM ANOVA framework. Since you only have two time points, why not just compute their difference then use a typical design? On 10/11/19 2:34 PM, miracle ozzoude wrote: External Email - Use Caution Hello Experts, I would like to include covariates in the

Re: [Freesurfer] brain mask without CSF ...

of BOLD signal (of soft tissues outside the skull) and crisp movements (rotations, roll) of the head during the recording, but I can be wrong; any further hint is really appreciated best stefano Il 11 ottobre 2019 alle 0.55 "Greve, Douglas N.,Ph.D." <mailto:dgr...@mgh.harvard.edu

Re: [Freesurfer] Mri_mask producing only zeros

Can you send the full command line (the one below does not make sense)? And send the terminal output On 10/14/19 11:53 AM, Sims, Sara A (Campus) wrote: External Email - Use Caution Freesurfers, I am trying to use mri_mask using surface overlays. I made a label into a volume and then int

Re: [Freesurfer] Learning dti processing tutorial

Sorry, you will have to figure this out for yourself. On 10/18/2019 5:02 PM, Renew Andrade wrote: External Email - Use Caution I am using a database of NITRC repository https://www.nitrc.org/projects/parktdi/ . This images have a nifti file for 1000s/mm^2 and 2500s/mm^2. I don’t know i

Re: [Freesurfer] time point exlusion file exceed nframes

Hi Lauri, I think this comes down to whether you start counting from 0 or 1. FSFAST starts from 0, so the time of  time point N is N*TR. The maximum you can have is N=208, and so the max time would be 478.4. Your 480.7 exceeds this limit. doug On 10/23/2019 1:34 PM, Lauri Tuominen wrote: >

Re: [Freesurfer] Learning fsfast tutorial

look in sess01/bold, you should see 001 and 002. Do you? On 10/22/2019 9:40 AM, Renew Andrade wrote: External Email - Use Caution Dear experts: I am trying to run preproc-sess -s sess01 -fsd bold -stc up -surface fsaverage lhrh -mni305 -fwhm 5 -per-run But the outcome is ERROR: no run d

Re: [Freesurfer] recon-all at native resolution

gt; Is this expected when running -conf2hires? > > Jim > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > On Behalf Of Greve, Douglas N.,Ph.D. > Sent: Tuesday, October 15, 2019 11:54 AM > To: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer

Re: [Freesurfer] Learning fsfast tutorial

You have to have the directory structure set up properly. You can put task and rest in the same session or in different sessions On 10/24/19 9:43 AM, Renew Andrade wrote: > > External Email - Use Caution > > Dear FreeSurfer experts: > I am trying to use my own data so I don’t have the sam

Re: [Freesurfer] subcortical volume-based pet analysis

On 10/21/19 10:24 AM, miracle ozzoude wrote: > > External Email - Use Caution > > Hello Experts, > > I do have couple questions about using mri_glmfit and mri_glmfit-sim > for this analysis based on the tutorial page. > https://surfer.nmr.mgh.harvard.edu/fswiki/PetSurfer >  1) Do i have

Re: [Freesurfer] Getting stats from stats files. rh.w-g.pct. asegstatsdiff

On 10/22/19 9:00 AM, Троицкий Антон Александрович wrote: > External Email - Use Caution > > Dear free surfer developers, > > > 1. > > I processed several items of data. And I have rh.w-g.pct file in my stats > folders. > > How can I get process this file to get table reading file? I tri

Re: [Freesurfer] Error in glmfit-sim cache

I don't know what this refers to On 10/18/19 4:45 PM, Renew Andrade wrote: > External Email - Use Caution > > I have tried all the values it pinpoints to but none seem to work. > > ___ > Freesurfer mailing list > Freesurfer@nmr.mgh.harvard.edu >

Re: [Freesurfer] FSGD file formatting for Xhemi

ffected and > unaffected hemispheres in stroke patients. > > Thanks in advance > > On Fri, Oct 18, 2019 at 3:57 PM Greve, Douglas N.,Ph.D. > mailto:dgr...@mgh.harvard.edu>> wrote: > > What are you trying to test? Usually you don't have lh and rh in >

Re: [Freesurfer] Converting ROIs from MNI152 space to MNI305

try something like mri_label2vol  --reg $FREESURFER_HOME/average/mni152.register.dat --seg your.mni152.roi.nii.gz --temp $FREESURFER_HOME/subjects/fsaverage/mri/orig.mgz --o your.mni152.roi-in-mni305.nii.gz On 10/21/19 12:42 PM, Barbour, Tracy,M.D. wrote: > > Hello experts, > > I am trying to

Re: [Freesurfer] how to get the full name of cortical segmentation structures?

For the aparc see Desikan, NI 2006, An automated labeling system for subdividing the human cerebral cortex on MRI scans into gyral based regions of interest For the a2009s, see Destrieux, NI 2010, Automatic parcellation of human cortical gyri and sulci using standard anatomical nomenclature O

Re: [Freesurfer] Mean p-value of uncorrected cluster in Qdec

In the qdec analysis it is hard because we don't really support qdec anymore. You can run the command-line stream, and when you run mri_glmfit-sim to do the clustering, set --cwp 1 to keep all the clusters. At that point you can use mri_segstats with --i sig.mgh and --seg ocn.mgh (where ocn is

Re: [Freesurfer] Mri_mask producing only zeros

Can you send the full terminal output? On 10/14/19 12:01 AM, Sims, Sara A (Campus) wrote: > > External Email - Use Caution > > Freesurfers, > > I am trying to use mri_mask using surface overlays. I made a label > into a volume and then into a surface with 1s inside the label and 0s > out

Re: [Freesurfer] recon-all at native resolution

ns and we're were hoping that the higher resolution > images would help. The surfaces look fine. > > We should use the -hires flag instead in this scenario? > > Thx. > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > On Behalf Of Greve, D

Re: [Freesurfer] recon-all at native resolution

? > > Is my thinking correct? If so, which flag is best? > > Jim > > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > On Behalf Of Greve, Douglas N.,Ph.D. > Sent: Thursday, October 24, 2019 5:37 PM > To: freesurfer@nmr.mgh.harvard.edu &

Re: [Freesurfer] view labels in native space

yes, the vertices in one subject do not have any correspondence to vertices in an other subject On 10/25/19 12:08 PM, Nasiriavanaki, Zahra wrote: Hi Freesurfer experts I have a few labels that correspond to activation clusters in fsaverage space for an individual subject. I used mri_label2label

Re: [Freesurfer] recon-all at native resolution

-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. Sent: Friday, October 25, 2019 11:17 AM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subjec

Re: [Freesurfer] b0 to T1’s co-registration without b0 inhommogeneities

12 DOF is probably not going to help much. I vaguely remember that there were some tools out there that would attempt to fit the non-linear parts of the B0 map. Maybe in fmriprep? Sorry, can't give you more guidance than that. On 10/26/19 10:56 AM, Daniel Callow wrote: External Email -

Re: [Freesurfer] Vertex and voxel-wise linear regression in Freesurfer

what is your request? On 10/26/19 1:20 PM, Larry Lai wrote: External Email - Use Caution Hello FreeSurfer Users I'm attempting to explore the correlations between the surface-based and voxel-based values and adjusted for nuisance covariate in FreeSurfer. Correlational study: A. Cortic

Re: [Freesurfer] Error in glmfit-sim cache

Which version of FS are you using? One thing you can try is setenv LANG en_US.UTF-8 or if you on bash export LANG=en_US.UTF-8 On 10/26/19 2:56 PM, Renew Andrade wrote: External Email - Use Caution I don’t know what do you mean by not knowing what it means. I said that I have tried all

Re: [Freesurfer] mri_glmfit ill-conditioned matrix question

My guess is that your covariates have almost no range to them and so look like constant (similar to columns 1 and 2). You can try demeaning and rescaling the covariates. You can do this by hand and create a new FSGD file or you can add the following lines anywhere in the fsgd: RescaleFlag 1 Deme

Re: [Freesurfer] recon-all -skullstrip issues

Did you run recon-all from the beginning? It needs to create those files On 10/27/19 3:18 PM, Adam Rytina wrote: External Email - Use Caution Hello all, I´m struggling with running "recon-all -skullstrip", in general with "recon-all". I added NIfTI series file to a new directory "QWE"

Re: [Freesurfer] mri_glmfit ill-conditioned matrix question {Disarmed}

maging > >> On Oct 28, 2019, at 7:33 AM, Greve, Douglas N.,Ph.D. >> mailto:dgr...@mgh.harvard.edu>> wrote: >> >> My guess is that your covariates have almost no range to them and so >> look like constant (similar to columns 1 and 2). You can try >> d

Re: [Freesurfer] mri_glmfit ill-conditioned matrix question {Disarmed}

sion Neuroimaging > Staff Research Associate 1 > >> On Oct 28, 2019, at 11:17, Greve, Douglas N.,Ph.D. >> wrote: >> >> Yes >> >>> On 10/28/19 1:04 PM, Nillo, Ryan Michael R wrote: >>> Am I correct in assuming this results in z-scoring/normalizi

Re: [Freesurfer] recon-all -skullstrip issues

tutorial set and run recon-all on that? Thanks Adam Od: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> za uživatele Greve, Douglas N.,Ph.D. <mailto:dgr...@

Re: [Freesurfer] question about qdec 'Generate Stats Data Tables'

Sorry, we are not supporint QDEC any more. Try using asegstats2table separately. You can cut and paste the printed asegstats2table command into the shell On 10/29/2019 10:05 AM, ?? wrote: External Email - Use Caution Hello, We had a problem when using QDEC for group analysis. After g

Re: [Freesurfer] nuisance factors

You are almost there. In the first step, you would test for an interaction between age and diagnosis in the DODS model with: 0 0 0 0 1 1 -1 -1 If there is no interaction, then you can move to the DOSS model (which includes age) with contrast 0.5 0.5 -0.5 0.5 0 You need that last 0 to account fo

Re: [Freesurfer] FSGD file formatting for Xhemi

covariates when running mri_glmfit? Thanks in advance. On Fri, Oct 25, 2019 at 12:18 AM Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> wrote: If you are trying to determine whether the hemispheres are different, then you need to do the subtraction between the hemis (ie, the --pair

Re: [Freesurfer] Mapping coordinates from sphere file to ?h.white

I don't know what you mean by "expand this sphere to the fsaverage's white surface". I don't know what fsLR coords are. Please explain further On 10/28/2019 6:58 PM, Oscar Esteban wrote: External Email - Use Caution Dear experts, In the context of the BIDS transforms extension and the

Re: [Freesurfer] Matrix is ill-conditioned or badly scaled

The problem is that some of your groups are very small, eg, groups 2 and 4 only have 3 subjects. The way you have it set up, there are four parameters (offset and 3 slopes) for each group. Thus, you are running out of DOFs for those two groups (and not so much better on some of the others). On

Re: [Freesurfer] nuisance factors

can you send your command line, terminal output, and the fsgd file? On 10/30/19 4:23 PM, Georgina Angelopoulou wrote: > > External Email - Use Caution > > Thank you very much! That makes a lot of sense. > However, when I tried to run the analysis using that contrast (0.5 0.5 > -0.5 -0.5 0

Re: [Freesurfer] Cortical thickness values on a vertex base level

I'm not sure what you mean. Do you want the mean thickness of a cluster and/or its surface area? On 10/30/19 6:02 PM, Aicha Dijkshoorn wrote: > > External Email - Use Caution > > Dear developers, > > For a case-control study we are comparing the cortical thickness and > cortical surface

Re: [Freesurfer] Fwd: Fw: glm error

You are not creating the 4D_VOLUME_OUTPUT.lh.nii.gz  file correctly Try mri_concat --o 4D_VOLUME_OUTPUT.lh.nii.gz --i */Bold/PCC_Bold1_L/bilat*/pcc.nii.gz Where you have "bilat*", that should only be one folder On 10/31/19 12:04 PM, Amrita Bedi wrote: > > External Email - Use Caution >

Re: [Freesurfer] FSGD file formatting for Xhemi

advance. > > On Wed, Oct 30, 2019 at 3:01 PM Greve, Douglas N.,Ph.D. > mailto:dgr...@mgh.harvard.edu>> wrote: > > I don't understand. What per hemisphere variable? > > On 10/25/2019 3:15 AM, Jose Graterol wrote: >> >> External Email

Re: [Freesurfer] PETsurfer issue

The MGX method is only valid in voxels that have some gray matter in them (defined as 1% in the command line below), so any WM is set to 0 (probably accounts for the big hole that you see). The mgx output is divided into cortical GM and subcortical GM, so you are probably looking at the cortica

Re: [Freesurfer] Cortical thickness values on a vertex base level

> > ? > > > > 0.013 > > Left Fusiform gyrus > > > > ? > > > > ? > > > > ? > > > > 0.021 > > Right Paracentral lobule > > > > ? > > > > ? > >

Re: [Freesurfer] nuisance factors

You have to specify that this is a DOSS analysis with --fsgd CMTX_b.fsgd doss On 10/31/19 12:38 PM, Georgina Angelopoulou wrote: > > External Email - Use Caution > > Dear Douglas, > > Thank you once again for your reply and your help. > > Attached please find the fsgd file (CMTX_b.fsgd)

Re: [Freesurfer] Fw: glm error

subject and not sure how to go about this. On Thursday, October 31, 2019, Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> wrote: You are not creating the 4D_VOLUME_OUTPUT.lh.nii.gz file correctly Try mri_concat --o 4D_VOLUME_OUTPUT.lh.nii.gz --i */Bold/PCC_Bold1_L/bilat*/pcc.nii.gz Whe

Re: [Freesurfer] Fw: glm error

t mean correlation values to the seed from each individual subject and not sure how to go about this. On Thursday, October 31, 2019, Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> wrote: You are not creating the 4D_VOLUME_OUTPUT.lh.nii.gz file correctly Try mri_concat --o 4D_VOLUME_OUTP

Re: [Freesurfer] Fw: glm error

uot;Mean" column On 11/1/2019 12:16 PM, Amrita Bedi wrote: External Email - Use Caution Across all activations since the pcc map was generated by an osgm. On Friday, November 1, 2019, Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> wrote: you mean the average across

Re: [Freesurfer] nuisance factors

Yes, you can. Contrast for what? Also, in theory, there should not be a change in eTIV with age. The "e" in eTIV means "estimated" and sometimes the estimate can get non-sensensical aspects to it. On 11/2/19 12:33 PM, Georgina Angelopoulou wrote: > > External Email - Use Caution > > Than

Re: [Freesurfer] Subtraction of Stroke Volumes

So,you have the surface-based BA4 label and a surface-based lesion label. You want to create a new label of BA4 that excludes the lesion label. Is that right? On 11/4/19 11:17 AM, Rellick, Stephanie wrote: > > External Email - Use Caution > > Hi All, > > I am looking for some help. I am

Re: [Freesurfer] Longitudinal Analysis for functional connectivity data?

You can use the longitudinal anatomical analysis to inform the functional analysis across time, but there is not a longitudinal functional analysis per se. On 11/5/2019 2:15 PM, Barbour, Tracy,M.D. wrote: Hello Freesurfer experts! I see that there is a longitudinal processing pipeline for volum

Re: [Freesurfer] FSGD file formatting for Xhemi

o have all the affected just in one side (e. g. the left hemisphere). Thanks in advance. On Thu, Oct 31, 2019 at 7:10 PM Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> wrote: There are not any restrictions, just do the same as you would for a non-paired analysis. In any event, yo

Re: [Freesurfer] nuisance factors

If you are going to use the FSGD framework, you either have to have all covariates be DOSS or all be DODS, you can't have a mixture. If you want a mixture, then you need to create your own design matrix and then contrast matrix from that. Pass the design matrix to mri_glmfit with --X (and don't

Re: [Freesurfer] mri_surfcluster error -- FsFastTutorialV6.0

Did you create the "my-glm" folder? If so, what was your command? Can you send a link to the exact wiki page? On 11/6/19 2:49 AM, 王如雪 wrote: > > External Email - Use Caution > > > Hi Sir/Madam: > > I got an error when executing the new version "mri_glmfit-sim" > correction for multiple c

Re: [Freesurfer] Longitudinal Analysis for functional connectivity data?

gt; > Best, > > Tracy > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Greve, Douglas > N.,Ph.D. > *Sent:* Tuesday, November 5, 2019 3:22 PM > *To:* freesurfer@nmr.mgh.harvard.edu &

Re: [Freesurfer] T2 white matter surface refinement

No, right now only T1 is used to place the white/gray On 11/7/19 6:43 PM, Defenderfer, Matthew K wrote: > > External Email - Use Caution > > Hi, > > Looking through the documentation, there are extra options to include > a T2 image to refine the pial surface boundary, but I was wondering

Re: [Freesurfer] 4D multi-frame parcellation

When you say it is 4D, what do you mean? That each label has its own frame? On 11/6/19 5:59 PM, 曲岸 wrote: > > External Email - Use Caution > > Hi there, > > I am working with creating a surface parcellation from a volumetric > parcellation and have some questions as follows: > > 1. If the

Re: [Freesurfer] Question about design matrix for surface group analysis

yes, that looks right to me. On 11/8/19 1:28 AM, 邓刊 wrote: > > External Email - Use Caution > > Dear freesurfer users, > I have a question about the design matrix.We want to analyse the > relationship between the cortical thickness and the neuropsychological > test. We have two groups:TL

Re: [Freesurfer] Question about convert fsaverage to fsaverage5

Yes, mri_surf2surf. Run it with --help to see a bunch of examples. Write back if you still have questions On 11/8/19 3:05 AM, chenyang jiang wrote: > > External Email - Use Caution > > Dear Fs Developers > > Hi, I am new to freesurfer, after I ran the recon-all command, I want > to align

Re: [Freesurfer] FDR for aseg

You can run FDG like mri_fdr --i contrast/sig.mgh --fdr FDRVALUE where you set your desired FDRVALUE This will print out a threshold. You can then apply that threshold to your table On 11/8/19 6:57 AM, Benjamin Ineichen wrote: > > External Email - Use Caution > > Dear Freesurfer experts,

Re: [Freesurfer] Inconsistent Morphology Output

It should give consistent output when re-running. The first thing to check is that the version of FS has not changed. In general, you should NOT be using the development version. The second thing is to make sure that it is the FS output that is changing and not that something has changed in you

Re: [Freesurfer] low snr with t1_mp2rage compared to MPRAGE

What is a "t1_mp2rage_sag"? I know what an mp2rage is. Are you asking about the quantitative t1 output or the uni? On 11/9/19 6:57 AM, Knut J Bjuland wrote: > > External Email - Use Caution > > Dearfreesurferexperts, > > Ihavesomeimagethatareint1_mp2rage_sag.ArethereanythingIshouldbeaware

Re: [Freesurfer] surface group analysis with qdec

We are not supporting QDEC anymore. QDEC is running mri_glmfit, which you can run yourself from the command line. If you seek help, send the fsgd file and the Xg.dat design matrix On 11/11/19 7:07 AM, Ferraro, Pilar wrote: > > External Email - Use Caution > > Hi! > > I've previously run

Re: [Freesurfer] Fwd: Regarding Issue in reading binary files inside DICOM Directory

I have no idea what that image means. Have you tried using dcmunpack? You can pass it a folder and it should find all the dicoms in there On 11/9/19 11:03 PM, sudhakar Mishra wrote: > > External Email - Use Caution > > Hi, > > I am facing problem in reading dicom files arranged in a way d

Re: [Freesurfer] how to compute geodesic distance and intensity

recon-all outputs a gray/white contrast file (?h.w-g.pct.mgh). I don't know what you mean by geodesic distance. On 11/10/19 9:27 PM, chenyang jiang wrote: > > External Email - Use Caution > > Dear fs developer > > Hello, I want to compute Geodesic distance and intensity contrast in > all

Re: [Freesurfer] FSGD file formatting for Xhemi

erage as the target and not to > fsaverage_sym). > > On Tue, Nov 5, 2019 at 9:24 PM Greve, Douglas N.,Ph.D. > mailto:dgr...@mgh.harvard.edu>> wrote: > > what do you mean "flip" them? > > On 11/5/2019 6:10 AM, Jose Graterol wrote: >> >>  

Re: [Freesurfer] 4D multi-frame parcellation

2 is wrong. But the output is still wrong. Many thanks. Best, An Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> 于2019年11月11日周一 下午12:16写道： When you say it is 4D, what do you mean? That each label has its own frame? On 11/6/19 5:59 PM, 曲岸 wrote: > > External Email - Us

Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary file

It looks like you have one gigantic cluster with a value of -inf at vertex 41. How did you generate /fsdata/lme/thickness/rh.thickness.B1B7.mgh ? Have you looked at it in freeview? On 11/11/2019 7:39 PM, Bronwyn Overs wrote: External Email - Use Caution Dear Freesurfer Mailing List,

Re: [Freesurfer] Recon all hard failure,

And before that you should check the orig and white surfaces On 11/12/2019 9:37 AM, Bruce Fischl wrote: > Hi Vicente > > I'm not sure what the images are showing - maybe the inflated surface? > That isn't useful to look at in the volume. You should check the > inflated.nofix surface and see if som

Re: [Freesurfer] Question about how to create subjectname file during fMRI analysis

I can't see any of the images you posted. Can you repost with text instead? On 11/12/2019 8:45 AM, 于倩倩 wrote: External Email - Use Caution Dear Developer, I am learning the FaFast to analyse the fMRI data. I have a question about the sunjectname file, I created a text file under

Re: [Freesurfer] 4D multi-frame parcellation

rf independently, which command > should I use to get a register.dat file? > In addition, the intensity of the 4D fMRI dataset I have is between > [-1, 1] and not integers, would this cause any problem? > > Best, > An > > > On 11/12/19 10:41 AM, Greve, Douglas N.,Ph.D. wrot

Re: [Freesurfer] Max threshold marked as '-inf' in cluster summary file

esearch Assistant > > > Neuroscience Research Australia > Margarete Ainsworth Building > Barker Street Randwick Sydney NSW 2031 Australia > *M* 0411 308 769 *T* +61 2 9399 1725 > > > neura.edu.au <http://neura.edu.au/> > > Twitter <https://twitter.com/neurau

Re: [Freesurfer] Fwd: recon-all error: ltMNIreadEx: could not open file transforms/talairach.xfm

You did not tell recon-all to do anything:) Try adding -all to your command line On 11/13/19 2:10 PM, Dalton Bermudez wrote: > > External Email - Use Caution > > > > -- Forwarded message - > From: *Dalton Bermudez* > > Date: Wed, Nov 13, 2

Re: [Freesurfer] Processor speed/cores vs cache size

It is pretty complex. If you're only running one job at a time, then faster processor is better On 11/13/19 3:00 PM, Pradyumna Bharadwaj wrote: > > External Email - Use Caution > > Hello, > > For running recon-all or tracula on a local workstation, is it > recommended to go for a higher

Re: [Freesurfer] Spatial smoothing for cortical folding measures

Usually not for LGI. People usually don't use curv or sulc in group studies, so the question does not usually come up. For thickness, we usually use 5-10mm On 11/13/19 9:49 PM, huyang wrote: > > External Email - Use Caution > > Dear FS experts, > > Is it necessary to do spatial smoothing

Re: [Freesurfer] Volume (WM Parcellation) of RightCerebralCortex--Freesurfer 6.0

You can find it in aseg.stats under # Measure lhCortex, lhCortexVol, Left hemisphere cortical gray matter volume, 272816.537999, mm^3 # Measure rhCortex, rhCortexVol, Right hemisphere cortical gray matter volume, 260016.082731, mm^3 # Measure Cortex, CortexVol, Total cortical gray matter volume,

Re: [Freesurfer] Question about design matrix for surface group analysis

he neuropsychology  regressing out the effects of gender and age, but > I don't know how to make the design matrix? Is it [0.5 -0.5 0.5 -0.5 0 > 0 0 0 1 -1 1 -1 ] ? > > Best wishes, > Kan > > > > At 2019-11-12 01:18:10, "Greve, Douglas N.,Ph.D." > wrote

Re: [Freesurfer] Fw: surface group analysis with qdec

The problem is that all of your class=0 subjects have a 0 duration meaning that you cannot compute a duration slope for this class. In this special case, you can run a different-offset, same-slope analysis with --fsgd dur.fsgd doss Change your contrast matrix to 1 -1 0 On 11/14/19 9:47 AM, Fer

Re: [Freesurfer] 4D multi-frame parcellation

already > registered to its anatomical volume(by using others tools). The new 4D > volume that I tried and succeed is the volume not registered. > > I have no idea why the 4D volume after the transformation would cause > a failed result. Could you please let me know that? &g

Re: [Freesurfer] Multiple comparisons

My preferred method is to use permutation https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm On 11/14/19 12:29 PM, Juan Rivas wrote: > > External Email - Use Caution > > I would like to know how the correction is made for multiple > comparisons in the statist

Re: [Freesurfer] Questions for PetSurfer

On 11/15/19 4:19 AM, Soo-Jong Kim wrote: > > External Email - Use Caution > > Dear FreeSurfer experts, > > I am a student in neuroimaging using FreeSurfer. > I have some questions and I don't know where to send questions. > That's why I found this mail and writing. > > I've studied PetSur

Re: [Freesurfer] Cortical thickness values on a vertex base level

Best wishes, > AIcha > > *Van:* freesurfer-boun...@nmr.mgh.harvard.edu > namens Greve, Douglas > N.,Ph.D. > *Verzonden:* donderdag 31 oktober 2019 19:16 > *Aan:* freesurfer@nmr.mgh.harvard.edu > *Onderwerp:* Re: [Freesurfer] Cortical thickness values on a verte

Re: [Freesurfer] Question about the input for longitudinal processing pipeline

Do all images and time points have contrast? If some do and some don't, then I don't think you can properly do the analysis? On 11/15/19 10:06 AM, Darko Komnenić wrote: > > External Email - Use Caution > > Dear Freesurfer experts, > I wanted to run the Freesurfer's longitudinal processing

Re: [Freesurfer] Brain lobules pooling- request

sorry, it is not clear to me what is going wrong here. Did the mri_annotation2label command fail? or mris_anatomical_stats command? On 11/17/19 9:55 PM, Samson Nivins wrote: > > External Email - Use Caution > > Hi FreeSurfer Team, > >   I am interested in individual lobular volume and

Re: [Freesurfer] (no subject)

fer/BN_Atlas_246_LUT.txt' --no-xcerseg) > gives me only the cortical segmentation. Is there any way to also > include the subcortical segmentation based on my individual atlas? I > also have an Atlas_subcortex.gca file available. > > Best, > Boris > > On Tue, Aug 13, 2019

Re: [Freesurfer] 4D multi-frame parcellation

recon-all for the anatomical volume and saved all > outputs(mri,labels,surf and etc.) in the bert folder. I use it because > I need to specify the required flag -s in bbregister in order to > register the functional volume to its anatomical volume. > > Many thanks. > > Best, > A

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