Re: [Freesurfer] problem with mri_surfcluster

are in the file lh.MS075_R01_07_R1year.subjspace.mgh > > > Thanks, > > Vale > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Greve, Douglas > N.,Ph.D. > *Sent:* Monday, May 20, 2019 2:46:54 PM &

Re: [Freesurfer] problem with mri_surfcluster

e command) > > > > > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Greve, Douglas > N.,Ph.D. > *Sent:* Monday, May 20, 2019 2:56:38 PM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] problem with mri_surfcluster > Whe

Re: [Freesurfer] Moving data files

I don't think you need to worry about that. We move/copy subject folders all the time without incident or problem. On 5/20/19 3:49 PM, Mingzhu Hou wrote: > > External Email - Use Caution > > Dear Freesurfer team / community, > > This is a very basic and general question. I am currently se

Re: [Freesurfer] Mri glmfit sim error

You have applied a lot of smoothing, and the tables don't go up that high. Usually people will apply 5-10mm of smoothing. If you really want that much smoothing, you should use permutation. See https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/MultipleComparisonsV6.0Perm On 5/21/2019 10:09 A

Re: [Freesurfer] Mri glmfit sim error

te. On 5/21/19 10:43 AM, Amrita Bedi wrote: > > External Email - Use Caution > > Hi Dr Greve, > > Is it not possible to use Monte Carlo for 30 FWHM? > > Best, > Amrita > > On Tuesday, May 21, 2019, Greve, Douglas N.,Ph.D. > mailto:dgr...@mgh.har

Re: [Freesurfer] problem with mri_surfcluster

2surf to do it) > > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Greve, Douglas > N.,Ph.D. > *Sent:* Tuesday, May 21, 2019 10:31:57 AM > *To:* freesurfer@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] problem with mri_su

Re: [Freesurfer] mris_label2annot empty Annot

r-ow...@nmr.mgh.harvard.edu > <mailto:freesurfer-ow...@nmr.mgh.harvard.edu> > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of Freesurfer digest..." > > > Today's Topics: > >    1. Re: mkan

Re: [Freesurfer] Segmenting internal capsule

Those region numbers are just a placeholder. We don't segment the capsules. I can't find intcapseg, but it was very crude anyway. On 5/20/19 10:06 PM, Chinappen, Dhinakaran Maheswaran wrote: > Dear Freesurfer community experts, > > We're looking to segment the internal capsule using T1 data. We f

Re: [Freesurfer] number of vertices

mris_info lh.orig will do it On 5/21/2019 6:45 PM, Sam W. wrote: External Email - Use Caution Hi, How can I check how many vertices an image of my subject has? Best regards, Sam ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] question on surface analysis

On 5/22/2019 10:19 AM, Barletta, Valeria wrote: Dear Freesurfer, I have a surface file containing values of a cortical myelination index (rh.MS075_CME.mgh), and a lesion mask (rh.surf_CL03.mgh) What I need to do is: - Masking the surface file with the lesion mask, to create a new lesion mas

Re: [Freesurfer] question on surface analysis

to .mgh surface-based files? > > I cannot convert them to .nii and I think mri_binarize and > mri_segstats work only on volumes. > > > Thanks, > > Vale > > > > *From:* freesurfer-boun...@nmr.m

Re: [Freesurfer] Checking number of parcels after transformation of an annotation file into a .nii.gz file

the way that pops to mind is to use matlab a = MRIread('aparc.250+2mm.nii.gz'); u = unique(a.vol(:)); length(u) will give you the number of unique segmentation number (including 0) On 5/22/19 5:54 PM, Winkelbeiner, Stephanie A wrote: > > External Email - Use Caution > > Hi Freesurfers, >

Re: [Freesurfer] XL defect in recon-all

You can look at this tutorial https://surfer.nmr.mgh.harvard.edu/fswiki/FsTutorial/TopologicalDefect_freeview But if you are using high res, I would run high res stream I put together for the HCP: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp/ On 5/23/19 2:59 PM, Barletta,

Re: [Freesurfer] Error with mri_glmfit command

Can you send the Xg.dat file? On 5/23/2019 8:43 PM, Martin Juneja wrote: External Email - Use Caution Hi FS experts, I want to find clusters showing an association between cortical measures and behavior x6 (sex, age and variables x1-x5 as covariates). My FSGD file looks like: GroupDes

Re: [Freesurfer] XL defect in recon-all

oun...@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, May 23, 2019 3:46:30 PM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] XL defe

Re: [Freesurfer] 4 optseq2 questions

On 5/29/19 1:05 PM, Katarina Bendtz wrote: > > External Email - Use Caution > > Dear experts: > > > I'm using the optseq2 version 2.15 2009/05/26. I have three questions: > > > 1. How does the [PSDmin, PSDmax] relate to the jittered > intertrial intervals? > The PSDmax sets the maxi

Re: [Freesurfer] Error with mri_glmfit command

les within a class. > > > Thanks. > > > On Fri, May 24, 2019 at 9:42 AM Martin Juneja <mailto:mj70...@gmail.com>> wrote: > > Hi Dough, > > Please find the Xg.dat file attached here. > > Thanks. > > On Fri, May 24, 2019 at 7:30 AM

Re: [Freesurfer] "MATLAB: Undefined variable" error, FSFAST Tutorial, using Octave

Try just setting MATLAB to something so that it exists, eg, set MATLAB=1 export MATLAB On 5/28/19 5:08 PM, Zacharie Saint-Georges wrote: > > External Email - Use Caution > > > Dear Freesurfer Developers, > > > I am running into a "MATLAB: Undefined variable" error while doing the > FSFAS

Re: [Freesurfer] 4 optseq2 questions

On 5/31/2019 2:18 AM, Katarina Bendtz wrote: External Email - Use Caution Dear Douglas: Thank you so much for your reply. It is however still not clear to me how this works. Pls see my replies below. All the best and many thanks for your time, Katarina PS. I'm registered to the

Re: [Freesurfer] Fw: mri_aparc2aseg increases number of parcels? {Disarmed}

y 2019 6:23 PM > *To:* Freesurfer support list > *Subject:* Re: [Freesurfer] [EXTERNAL] Re: Checking number of parcels > after transformation of an annotation file into a .nii.gz file > > */External Email. Use Caution./* > > External Email - Use Caution > > That s

Re: [Freesurfer] FS recon-all issue "if: missing file name"

can you send the command line and full terminal output? Also, when you run it again, put -debug as the first argument. It will create a huge amount of terminal output, but it will be helpful for diagnosing the problem On 6/2/2019 3:57 AM, Kavinash Loganathan wrote: External Email - Use

Re: [Freesurfer] selxavg3-sess failed

It does not look like the error was captured in the log file. Can you send the full terminal output? On 6/2/2019 5:02 AM, starxifd wrote: External Email - Use CautionIt Hi, FS experts I got into trouble when running ’selxavg3-sess’ with a session id file. All sessions specified

Re: [Freesurfer] 4 optseq2 questions

The efficiency is low in part because you have only one presentation for each event type. The efficiency will scale with number of events for a given type and will decrease when you have more overlap in the HRFs. Whether it matters or not depends on how you are going to analyze your data. The op

Re: [Freesurfer] how to obtain a mean .mgh file

use mri_concat, eg, mri_concat lh.Ctrl*.fsaverage.mgh --mean --o mean.mgh On 6/4/2019 3:18 PM, Barletta, Valeria wrote: Dear Freesurfers, Is there a way to turn N .mgh files in to a single output .mgh file in which each vertex is the mean of the corresponding vertices in my input files? For e

Re: [Freesurfer] scan acquisition date from recon all

If you gave recon-all a dicom as an input, then it might be in there due to the conversion. On 6/6/2019 5:24 AM, Boris Rauchmann wrote: External Email - Use Caution Dear all, is there any way to find the scan acquisition date in the recon-all log? Thanks, Boris

Re: [Freesurfer] CSF MASK

No, not currently (next version) On 6/6/2019 12:57 PM, Marina Fernández wrote: External Email - Use Caution Dear Freesurfer experts, Is there any way to obtain a CSF mask in Freesurfer similar to that obtained with the SPM segmentation (see attached)? Thank you in advance. Best regard

Re: [Freesurfer] How to get the difference between orig.mgz and original image

Yes, mri_segstats will do it, but you need to sample the aseg into the native space. see https://surfer.nmr.mgh.harvard.edu/fswiki/FsAnat-to-NativeAnat On 6/8/2019 4:14 PM, Bruce Fischl wrote: Hi Jiachen I think mri_segstats includes the mean (and std) of the intensity within a structure so y

Re: [Freesurfer] Using mean thickness / total area as covariates

This is a question about the biology. I.e., when you include mean thickness as a covariate, you are then measuring the difference between groups subtracting out the mean thickness of each individual. By using a hemisphere specific value, you might introduce (or remove) cross-hemispheric effects.

Re: [Freesurfer] hippocampal subfield as CONN seeds

This will be a little tricky. How did you do the registration to MNI space? On 6/11/2019 1:36 AM, Nelson, Eric A wrote: External Email - Use Caution Hi all, I have successfully ran hippocampal subfields for a sample but would like to be able to use some of those subfields as seed region

Re: [Freesurfer] multi-slice timing correction

Sorry for the slow response (at OHBM). Yes, that sounds correct. If you pass it a file, then all other options are ignored. On 6/12/2019 7:12 AM, Joseph Dien wrote: External Email - Use Caution Okay, I looked through the source code itself and I think I worked it out. preproc-sess call

Re: [Freesurfer] translations and rotations from an affine transform matrix

If it is an LTA (not .dat file), you can use mri_coreg --mat2par ltafile There will be 9 values that come out: 1-3: translation in mm 4-6: rotation in deg 7-9: should all be 1s in this case On 6/20/2019 2:52 AM, Pfannmoeller, Joerg Peter wrote: Hello, is there a tool to extract the translations a

Re: [Freesurfer] Fwd: freesurfer picture

You will have to find the qdec output folder. There will be a subfolder for each contrast. Load the sig.mgh file in the contrast subfolder, eg, tksurferfv fsaverage lh inflated -aparc -overalay sig.mgh tksurferfv is just a convenient front end for freeview (fv) On 6/17/2019 1:56 PM, Abby tang wr

Re: [Freesurfer] Tksurfer and qdec: error sourcing and floating exception

tksurfer has some instabilities in it. It is obsolete and no longer being supported. Have you tried freeview? You can use tksurferfv which runs freeview with tksurfer options. On 6/12/2019 6:54 PM, Wafaa Sweidan wrote: External Email - Use Caution Hello all, I have been using freesurf

Re: [Freesurfer] bbregister- switched coronal and axial views error

What version of FS are you using? If before 6.0 (eg, 5,3), then it may be an error with the initialization. This is much improved in version 6. On 6/18/2019 5:38 PM, Wenzhen Zhao wrote: > External Email - Use Caution > > Dear list, > > After running preproc-sess on fmri data, bbr-sum was

Re: [Freesurfer] Within-subject vertexwise correlation

I'm not sure that this is a question we can answer. If you do smooth, then you should smooth both modalities the same amount. On 6/18/2019 10:12 PM, Matthieu Vanhoutte wrote: External Email - Use Caution Dear FS experts, I would like to compute within-subject correlation between two mo

Re: [Freesurfer] eTIV and brainmask mismatch on Philips data

If the registration looks ok then it probably means that the skull stripping was too aggressive. Have you looked at the skull stripping? On 6/14/2019 1:40 PM, Agnieszka Sabisz wrote: External Email - Use Caution Hi all! We are running FS v.6.0. on a supercomputer operating on Linux. We

Re: [Freesurfer] registration with bbr and determination of motion regressors with mcdat2mcextreg

That is fine. I don't think that there are any conventions you need to follow (it should just be an Nx6 matrix On 6/13/2019 8:45 PM, Pfannmoeller, Joerg Peter wrote: Hello, I have used bbr to register all EPI volumes in my time series to the brains of my participants. The fMRI time series at ea

Re: [Freesurfer] hippocampal subfield as CONN seeds

- Use Caution Thanks for your response, I believe CONN should be using SPM linear? Best, Eric From: Greve, Douglas N.,Ph.D. [mailto:dgr...@mgh.harvard.edu] Sent: Wednesday, June 12, 2019 8:27 AM To: Nelson, Eric A <mailto:eanel...@uab.edu> Subject: Re: [Freesurfer] hippocampal subfield as CO

Re: [Freesurfer] examining between group differences using DODS

On 6/7/2019 2:29 AM, Avi Gharehgazlou wrote: External Email - Use Caution Hi experts, I want to examine between-group differences in LGI controlling for age, sex and surface area (all except sex demeaned). To do so, I ran the DODS model on QDEC selecting: - “diagnosis” and “s

Re: [Freesurfer] Confirmation regarding running GLM on command line stream

Hi, sorry for the delay. On 6/7/2019 3:33 AM, Avi Gharehgazlou wrote: External Email - Use Caution Hi experts, Will you please confirm below command lines I run to examine between group differences in LGI? I have 3 questions listed. I can’t run the below line, it gives an error: mris_p

Re: [Freesurfer] translations and rotations from an affine transform matrix

you can also use lta_convert to convert a .dat file to an LTA On 6/22/2019 2:12 AM, Greve, Douglas N.,Ph.D. wrote: If it is an LTA (not .dat file), you can use mri_coreg --mat2par ltafile There will be 9 values that come out: 1-3: translation in mm 4-6: rotation in deg 7-9: should all be 1s in

Re: [Freesurfer] 4dfp data format

I don't know. I'm cc'ing Avi. On 6/8/2019 1:04 AM, Francesca Pentimalli wrote: External Email - Use Caution Dear freesurfer experts, I am trying to use the 4dfp data format, but I am not able to find the 4dfp suite of tools developed by Dr. Avi Snyder. Can someone please point me in th

Re: [Freesurfer] Within-subject vertexwise correlation

s the same amount. The question is whether I should or not smooth before calculating within-subject correlation? Best, Matthieu Le sam. 22 juin 2019 à 02:14, Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> a écrit : I'm not sure that this is a question we can answer. If you do smo

Re: [Freesurfer] Group mean tracer uptake images

you can use something like mri_concat overlay1.mgh overlay2.mgh --mean --o mean.overlay.mgh On 6/22/2019 4:18 PM, Boris Rauchmann wrote: > External Email - Use Caution > > Dear FS community, > > how can I create group mean tracer uptake images in surface space with FS > from several over

Re: [Freesurfer] WARNING: no voxels in AR1 computation

This is not a problem with the contrasts, it is an issue with the mask. How did you create the mask? Can you send the full terminal output? On 6/21/2019 6:16 PM, Francesca Pentimalli wrote: External Email - Use Caution Dear FreeSurfer experts, I am trying to run mri_glmfit on a series

Re: [Freesurfer] question for preprocessing

It does 1-3. It also labels cerebellum which you could then use to perform #4 On 6/23/2019 7:03 AM, ping cao wrote: External Email - Use Caution Dear expert， Thank you for reading! I want to do these four pre-processing steps: 1. Re-sampling each MR image to 256*256*256; 2. Using the N

Re: [Freesurfer] Labelling SurfStat p-value surface map

It is probably using a tcsh shell to do the compression. Try using MRIwrite instead. You will have to create an mri structure. The easiest way to do that is to mri_convert lh.thickness template.mgh then read the template in to matlab template = MRIread('template.mgh'); template.vol = yourdata MRIw

Re: [Freesurfer] DesikanKilliany ROI for mri_glmfit

each individual subject to reference with > mri_glmfit? > > > *From:* Tammi Kral > *Sent:* Friday, June 21, 2019 9:18:46 PM > *To:* Greve, Douglas N.,Ph.D. > *Subject:* Re: [Freesurfer] DesikanKilliany ROI for mri_glmfit >

Re: [Freesurfer] mri_glmfit will not use mask or label

Try running it without --cortex On 6/26/19 4:57 PM, Jennifer Legault wrote: > > External Email - Use Caution > > Hi Freesurfer experts, > > I'm trying to constrain my sMRI analysis to only search for brain > regions (GMV) that are correlated with a behavioral measure within a > mask (mad

Re: [Freesurfer] converting correlation coefficient file into a table

If you want to compute FC between ROIs, then try fcseedcor. Run with -help to get more info On 6/27/19 11:42 AM, Wenzhen Zhao wrote: > External Email - Use Caution > > Dear List, > > I finished first level analysis of functional connectivity of all subjects > with respect to Left hippoc

Re: [Freesurfer] Area information on certain views

You mean the cross sectional area? I don't think we have tools to do that, though you might be able to do it in matlab. On 6/27/2019 11:02 PM, Kim, Jisoo,M.D. wrote: Dear freesurfer team, I searched the archives, but couldn't find this kind of question. I've used the brainstem segmentation

Re: [Freesurfer] Question about OptSeq

No, there is not. optseq assumes you will be doing an FIR analysis (=finite impulse response = not assuming a shape to the hemodynamic response). In this analysis, this must be the relationship. If you assume a shape, then this relationship is not necessary. In your case, you can set the dPSD=1

Re: [Freesurfer] Surfaces with different numbers of vertices.

Who did you create lh.test.nii? On 7/1/2019 1:47 PM, Nillo, Ryan Michael R wrote: Hi Bruce, We wanted to map values from a previous analysis to a representation of the brain with the sulci filled — something that resembles the output lh.pial-outer-smoothed from the recon-all -localGI. I tried u

Re: [Freesurfer] Surfaces with different numbers of vertices. {Disarmed}

lh.probability.nii is a probability mask created from about 63 subjects. Thanks in advance for the help, Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging On Jul 1, 2019, at 11:13 AM, Greve, Douglas N.,Ph.D

Re: [Freesurfer] Surfaces with different numbers of vertices. {Disarmed} {Disarmed}

calGI. Ryan Michael Nillo Staff Research Associate I University of California San Francisco Department of Radiology and Biomedical Imaging On Jul 1, 2019, at 11:41 AM, Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> wrote: how was pial-outer-smoothed create? On 7/1/2019 2:33 PM,

Re: [Freesurfer] mri_gtmpvc -- Failed tissue type check

Hi Cristina, can you send more info? Eg, your command line and terminal output. Do you do anything special (eg, your own annotation)? On 7/1/2019 5:57 PM, Lois Gomez, Cristina wrote: Hi Freesurfers, I am having trouble with one subject's PVC (we process many cases and never had this issue befor

Re: [Freesurfer] Question about OptSeq

problem with setting the dPSD to arbitrarily small values for an FIR analysis is that your statistical power drops by a factor of TR/dPSD > > Best. > > Davide > > *From:*Davide Nardo > *Sent:* 01 July 2019 18:38 > *To:* 'Greve, Douglas N.,Ph.D.' > *Subject:* RE

Re: [Freesurfer] Differing T1 Acquisition Comparison In Freesurfer

You're probably ok if design is balanced across scanner. So if you had two groups that you want to compare, you should make sure that they are represented equally across scanner. On 7/3/2019 9:56 AM, Keith, Kathryn wrote: > External Email - Use Caution > > Hi Bruce, > > Thanks so much f

Re: [Freesurfer] Qdec Message to Mailing List

yes, qdec can only have 2 factors with 2 levels. both qdec and mri_glmfit are linear methods (in fact, qdec just calls mri_glmfit). On 7/3/2019 9:39 AM, Marie Hill wrote: External Email - Use Caution Dear Sir/Madam, Could I post the following message to the mailing list: I am running

Re: [Freesurfer] Qdec Message to Mailing List

the continuous variable Age. Kind regards, Marie 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...@

Re: [Freesurfer] Qdec Message to Mailing List

rfer-boun...@nmr.mgh.harvard.edu> on behalf of Greve, Douglas N.,Ph.D. <mailto:dgr...@mgh.harvard.edu> Sent: 03 July 2019 16:22 To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Qdec Message to Mailing List can you send the command line, full te

Re: [Freesurfer] Single SUVr for PETsurfer

The mean over what area? Whole brain or just cortex? On 7/3/2019 2:15 PM, miracle ozzoude wrote: External Email - Use Caution Hello Expert, How do i get a single SUVr value for PETsurfer? Similar to Mean_Thickness from Freesurfer, I want to extract a global/Mean SUVr value for each of

Re: [Freesurfer] Qdec Message to Mailing List

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: 03 July 2019 16:22 To: freesurfer@nmr.mgh.harvard.edu

Re: [Freesurfer] Single SUVr for PETsurfer

gtm.stats file On 7/3/2019 3:36 PM, miracle ozzoude wrote: External Email - Use Caution Over the cortex. On Wed, Jul 3, 2019 at 2:59 PM Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> wrote: The mean over what area? Whole brain or just cortex? On 7/3/2019 2:15 PM, m

Re: [Freesurfer] Single SUVr for PETsurfer

)) _ __ (# of voxels in ROI 1 + .. # of voxels in ROI 68) On Wed, Jul 3, 2019 at 3:45 PM Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> wrote: You can look in the gtm.stats file for all the cortical ROIs. Multiply the uptake value by the number of voxels in t

Re: [Freesurfer] Error in mris_convert thickness file from ascii format

Why do you want to convert it to ascii? We have tools that will smooth it. In any event, you need something like mris_convert -c lh.thickness lh.white lh.thickness.asc On 7/3/2019 6:47 PM, Jee Su Suh wrote: External Email - Use Caution Hello, I am trying to convert ascii files conta

Re: [Freesurfer] make_average_subject error: could not load norm volume from (null)

Can you send the full terminal output of make_average_subject? There should also be some log files (make_average_volume.log and make_average_surface.log) in the average subject that would be helpful On 7/4/2019 4:36 AM, Mads Jensen wrote: External Email - Use Caution HI FreeSurfer Deve

Re: [Freesurfer] pial.lgi

did you run the lgi analysis? On 7/9/19 4:15 PM, vittal korann wrote: > > External Email - Use Caution > > Hi FS experts, > > I wanted to run the gyrification index for all patients with Schizophrenia > and volunteers. When I entered the command: > "recon-all -s SATM124  -qcache -measure p

Re: [Freesurfer] Desikan atlas

No. But you can just recon-all the mni152 and it will generate an aparc+aseg with the DK atlas On 7/9/19 1:59 AM, Pinar Pnr wrote: > > External Email - Use Caution > > Hi dear Freesurfer users, > > Is there a version of Desikan atlas in MNI space? > > Bset Regards, > Pinar > > > _

Re: [Freesurfer] Error in analyze (Qdec)

Can you tar or compress /home/abby/Desktop/qdecyoung/qdec/Untitled/ and upload it here ftp://surfer.nmr.mgh.harvard.edu/transfer/incoming Let me know when it is there and what the file name is On 7/9/19 6:35 AM, Abby tang wrote: > > External Email - Use Caution > > Hello FreeSurfer Develo

Re: [Freesurfer] Petsurfer: PET -> MNI305 problem

Did yyou check the tal registration of the subjects as created by recon-all? tkregister2 --mgz --s subject --fstal --surf orig On 7/10/19 2:32 PM, Eckbo, Ryan wrote: > > Hi Doug and experts, > > We're interested in running a voxel wise test-retest reliability > analysis on a set of PBR28 PET i

Re: [Freesurfer] FW: Trouble viewing files on tkmedit

Try using freeview (or tkmeditfv, a tkmedit command-line-style frontend for freeview). tkmedit is depricated. On 7/11/19 10:55 AM, Valerio, Kate wrote: > > External Email - Use Caution > > I was attempting to view some of our images and kept receiving this > error message (shown below). 

Re: [Freesurfer] Different template between FSFAST and SPM?

is this an individual or group? what version of FS are you running. On 7/11/19 11:10 AM, Zhi Li wrote: > > External Email - Use Caution > > Dear Freesurfer experts, > > Now I am using both FSFAST and SPM to preprocessed my functional image > data. In FSFAST, I replaced the subcortical tem

Re: [Freesurfer] Different template between FSFAST and SPM?

-Linux-centos6_x86_64-stable-pub-v6.0.0-2beb96c. Best, Lizhi On Thu, 11 Jul 2019 at 11:55, Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> wrote: is this an individual or group? what version of FS are you running. On 7/11/19 11:10 AM, Zhi Li wrote: > > External Email -

Re: [Freesurfer] mri_gtmpvc -- Failed tissue type check

;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: Monday, July 1, 2019 6:22 PM To: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu&g

Re: [Freesurfer] Paired Analysis Questions

On 7/13/2019 11:47 AM, FAST Study wrote: External Email - Use Caution Dear Dr. Greve: Hooray! All has run successfully for the Paired Analysis (https://surfer.nmr.mgh.harvard.edu/fswiki/PairedAnalysis). I used the [1 0] contrast to examine whether there are different within-group chan

Re: [Freesurfer] CSF mask

You can try running gtmseg. You will not want its final output, but along the way it will produce a file called apas+head.mgz, and this will have a semi-good segmentation of extracerebral CSF. On 7/12/2019 12:14 PM, Laboratorio de Neurociencia Funcional wrote: External Email - Use Cau

Re: [Freesurfer] Error in analyze (Qdec)

files? I have uploaded it in ftp, the file name is QDEC.tar.gz. Hope you can help me. Thank you very much. Abby Abby tang mailto:abbytang0...@gmail.com>> 于2019年7月10日周三 上午9:46写道： Hi I have uploaded it in ftp, the file name is /home/abby/QDEC.tar.gz or QDEC.tar.gz. Thank you. Greve, Dou

Re: [Freesurfer] mri_glmfit residualized data after motion correction

You will need to create your own design matrix that includes both the "QA" terms (which I think are just a constant, linear, and quadradic terms) and your motion regressors. The QA terms you can see in the Xg.dat file. Once you have a design matrix (in simple text/ascii format), you can pass it

Re: [Freesurfer] Petsurfer: PET -> MNI305 problem

I'm not sure I understand. It seems like the picture is misoriented but then you say that bbpet2anat.lta is correct because you applied it to the mgx.gm.nii.gz and it is aligned with the orig. On 7/10/2019 2:32 PM, Eckbo, Ryan wrote: Hi Doug and experts, We're interested in running a voxel wis

Re: [Freesurfer] CSF mask

Neurociencia Funcional wrote: External Email - Use Caution Thank you, Doug. The voxel resolution of the apas+head.mgz file is 1mm3. Would it be possible to obtain the same file but with the native resolution? Best, Jose El lun., 15 jul. 2019 a las 6:01, Greve, Douglas N.,Ph.D. (<mailto:

Re: [Freesurfer] Create no-skull brain with gray matter mask

The ribbon.mgz file should be about the same (but for both hemis) On 7/15/2019 9:36 AM, Bruce Fischl wrote: Hi Marina if you have a pial surface you can use mris_fill to fill the interior then use that as a mask cheers Bruce On Mon, 15 Jul 2019, Marina Fernández wrote: External Emai

Re: [Freesurfer] Question about coordinates in Freesurfer

For question 1, try this https://surfer.nmr.mgh.harvard.edu/fswiki/CoordinateSystems You did not say which MNI space you were dealing with (we use mni305, not 152). On 7/15/2019 12:02 PM, Zhi Li wrote: External Email - Use Caution Thank you very much, Tim. Any idea for the 1st question?

Re: [Freesurfer] optseq2 parameters setup

On 7/15/2019 12:50 PM, Tugce Duran wrote: External Email - Use Caution Hi Dr. Greve, I am interested in designing the Face Name Associative Memory Exam (FNAME) fMRI task for our study. There are 80 face-name pairs that we will use and the duration can be between 3.5 and 4.75 secs. I

Re: [Freesurfer] A Question Regarding Topology Correction

It does not sound like something we can do, though I don't entirely follow everything that you wrote On 7/10/2019 11:07 PM, Maedeh Khalilian wrote: External Email - Use Caution Dear FreeSurfer experts, I know that FreeSurfer does segmentation, surface reconstruction and topology corre

Re: [Freesurfer] make_average_subject error: could not load norm volume from (null)

Jensen wrote: External Email - Use Caution Thank you very much for spending time on this! I have attached the make_average_volume.log and make_average_surface.log files. Den man. 8. jul. 2019 kl. 16.44 skrev Greve, Douglas N.,Ph.D. <mailto:dgr...@mgh.harvard.edu>: Can you send th

Re: [Freesurfer] How to Divide the Surface Parcellations of the Brain

Can you use mris_divide_parcellation On 7/8/2019 1:27 PM, Mahshid Fouladivanda wrote: External Email - Use Caution Dear Bruce, All the outputs are .nii and .gii I do not know if it is possible to convert it to the annotation! By the way, what is needed for creation of the annotation fi

Re: [Freesurfer] Viewing Uncorrected Significance Map in Freeview

Try changing the thresholds (via the Configure button). When it first loads, the thresholds are set very low. When they get changed to your values (4,5), then there is nothing left and it looks like a blank brain. On 7/6/2019 9:38 AM, Marie Hill wrote: External Email - Use Caution Hi e

Re: [Freesurfer] optseq2 parameters setup

ase notify the person > listed above immediately by e-mail, and delete the original message > and attachments. > > *From:*Greve, Douglas N.,Ph.D. > *Sent:* Monday, July 15, 2019 11:03 PM > *To:* Tugce Duran ; Freesurfer support list > > *Subject:* Re: optseq2 parameters

Re: [Freesurfer] need for help

Don't use --inflated. The inflated surface is not a biological surface. The default is the white surface, which is the one you want (--projfrac 0.5 will project it to the middle between the white and pial) On 7/16/2019 11:34 AM, Reza Rahmanzadeh wrote: External Email - Use Caution Dear

Re: [Freesurfer] Pixel values in Brainstem segmentation {Disarmed}

mri_info --res file.mgz is probably better than mri_convert On 7/16/19 11:43 AM, Iglesias Gonzalez, Eugenio wrote: > > External Email - Use Caution > > Hi again, > > mri_convert will give you the voxel size, which is isotropic. Multiply > 2 of the dimensions and you’ve got the area. > > A

Re: [Freesurfer] need for help

te, mris_sphere ... > > > Do you think that means the output of mri_vol2surf is not correct, or > otherwise i could proceed with that , even when tksurfer could not > open it, for GLM in Qdec? > > > Thanks, > > Reza > > ------

Re: [Freesurfer] need for help

; Run mri_vol2surf with --help and look for --projfrac-avg > > > thanks a lot, > > Reza > > > > *From:* Greve, Douglas N.,Ph.D. > *Sent:* Tuesday, July 16, 2019 6:22:56 PM > *To:* Reza Rahmanzadeh; f

Re: [Freesurfer] need for help

rfer/subjects/FSP025//surf/lh.sphere* > * > * > * > * > What is the problem with my mris_preproc command-line? > > Reza > > -------- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Greve, Douglas > N.,Ph.D. > *Sent:* Tuesday, July 16, 20

Re: [Freesurfer] need for help

last argument, but again i got the error: >> Reading source surface reg >> /usr/local/freesurfer/subjects/FSP010/surf/lh.sphere.reg >> Loading source data >> No such file or directory >> ERROR: could not read /usr/local/freesurfer/subjects/FSP010/surf/lh.white as >

Re: [Freesurfer] need for help

-- > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Reza Rahmanzadeh > > *Sent:* Wednesday, July 17, 2019 4:26:21 PM > *To:* Greve, Douglas N.,Ph.D.; Freesurfer support list; > gr...@nmr.mgh.harvard.edu > *Subject:* Re: [Freesurfer] need for help &g

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

There is a program called tksurferfv that runs freeview but takes all the same command line args as tksurfer On 7/18/19 10:56 AM, Bruce Fischl wrote: > Hi Matthieu > > tksurfer has been deprecated for years. Is there a reason you can't > switch to freeview? > > cheers > Bruce > On Thu, 18 Jul 201

Re: [Freesurfer] voxel coordinates of corpus collosum

you can try mri_vol2label On 7/17/19 11:16 PM, Sadia Sheikh wrote: > > External Email - Use Caution > > Hello Bruce > > I don't have much experience in Freesurfer and I want to get the > labels of CC. Is there any other way to get corpus callosum labels or > voxels without using Matlab?

Re: [Freesurfer] Cluster sizes discrepancy for mri_surfcluster vs mri_segstats

When you run mri_surfcluster, save an output cluster number (--ocn) output, then feed that into mri_segstats. On 7/18/19 11:44 AM, Mark Wagshul wrote: > > External Email - Use Caution > > Hi.  I have a question about cluster size determination within Freesurfer. > > We are running linear

Re: [Freesurfer] voxel coordinates of corpus collosum

command or this command is not possible for corpus callosum? Please find the attached output of the command line. On Fri, Jul 19, 2019 at 12:25 AM Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> wrote: you can try mri_vol2label On 7/17/19 11:16 PM, Sadia Sheikh wrote: > >

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