Re: [Freesurfer] Fill holes in BOLD surface

how did you creaet this? On 12/20/2019 10:10 AM, Marina Fernández wrote: External Email - Use Caution Hi Freesurfer experts, I have projected 4D-preprocessed BOLD data to Freesurfer cortical surfaces. Resulting individual surfaces have many holes (see attached image) that I would

Re: [Freesurfer] mapping the reliability of separating GM/WM

The surf/?h.w-g.pct.mgh is a map of the white-gray percent difference On 12/20/2019 9:13 AM, Bruce Fischl wrote: sure, you should be able to make vertex-wise maps. I think Doug wrote something to do this, but if not I can modify mri_cnr to output mean and variance maps for gray and white easily

Re: [Freesurfer] matlab output issue

It says that there is only one time point in that data. Are you sure that run is fMRI? Try mri_info 007/f.nii.gz and see how many time points it has On 12/20/2019 8:56 AM, Baptista, Paulo wrote: External Email - Use Caution Hello FreeSurfer Developers, I'm helping researchers test

Re: [Freesurfer] Obtaining pre values from longitudinal dataset without cross-base-long

Yes, that will work On 12/21/2019 11:45 AM, Tudor Popescu wrote: External Email - Use Caution Dear FS experts, From a pre- data set, is it possible to extract thickness values at those two time points just by using recon-all, that is, without running the full longitudinal processing

Re: [Freesurfer] highres fMRI selxavg error

Why are you combining them into one bold folder? On 12/30/2019 9:09 AM, Nasiriavanaki, Zahra wrote: Dear Freesurfer experts Happy Holidays! I have a subject with two highres fMRI scan sessions. Attached you can see an image, showing how I organized the sub-folders. I preprocessed the bold1 and

Re: [Freesurfer] FSFAST registration

On 12/30/2019 7:55 PM, Star Xi wrote: External Email - Use Caution Dear FS experts, I’m processing the task-related fMRI using FS-FAST. I check the quality assurance and modified some subjects’ registration file(named new one as “register_manual.lta”). Then I do the first level

Re: [Freesurfer] mkanalysis-sess.new not found

Use mkanlaysis-sess. Why are you trying to use the .new version? On 12/31/2019 5:45 AM, Marco Ninghetto wrote: External Email - Use Caution Dear experts, my name is Marco and I'm using freesurfer to perform retinotopy analysis and I am having a problem with command:

Re: [Freesurfer] vol2subfield

Copy it to $FREESURFER_HOME/bin (or anywhere in your path) Make sure to make it executable with chmod a+x vol2subfield On 12/30/2019 6:57 PM, std...@virgilio.it wrote: External

Re: [Freesurfer] Problem for mri_glmfit

the ICV has a very different scale than the rest of the variables. Try subracting the mean and dividing by the stddev to bring it within range of the other variablse On 12/24/2019 12:58 PM, Gwang-Won Kim wrote: External Email - Use Caution Dear Sir, I ran "mri_glmfit" commend. I had

Re: [Freesurfer] Thickness problem

sig = -log10(p)*sign(contrast), so if p=.01, then sig=2. The sign(contrast) is the direction of the contrast On 12/19/2019 4:14 PM, Gwang-Won Kim wrote: External Email - Use Caution Hi Dr. Greve, Thank you for your comment. I compared cortical thickness bewteen two groups. I have a

Re: [Freesurfer] Manual segmentation to volume

space as target volume for my manual segmentation example.mgz? Many thanks! /Ben Am Mi., 18. Dez. 2019 um 20:19 Uhr schrieb Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>>: in this case, I might try mri_vol2vol, something like mri_vol2vol --fstal 1 --interp nearest --mov examp

Re: [Freesurfer] Creating a label from overlapping cluster results

There is a script called labels_intersect. I have not run it before, but the name would indicate that it would do the right thing On 12/19/2019 9:49 AM, Bruce Fischl wrote: Hi Cody not sure we have a binary for this, but it would be about 5 lines of matlab code cheers Bruce On Thu, 19 Dec

Re: [Freesurfer] Conversion fMRI volumes to surface

Please send the command line and full terminal output. Also, please include the previous emails doug On 12/19/2019 4:28 AM, Marina Fernández wrote: External Email - Use Caution Thanks Doug. I created the surface with the command line that I sent you (mri_vol2surf ...) and then, I run

Re: [Freesurfer] Project functional region into white matter

yes, either should work. On 12/18/19 3:15 PM, Corinna Bauer wrote: > > External Email - Use Caution > > Would it be best to do option 1 in the CVS space or in subject space? > > On Wed, Dec 18, 2019 at 2:57 PM Greve, Douglas N.,Ph.D. > mailto:dgr...@mgh.harvard.edu

Re: [Freesurfer] Project functional region into white matter

er > result, since the second would dilate in all dimensions. > I'll let you know if I run into any trouble with it. > > Thanks again, > > Corinna > > > On Wed, Dec 18, 2019 at 2:45 PM Greve, Douglas N.,Ph.D. > mailto:dgr...@mgh.harvard.edu>> wrote: > &

Re: [Freesurfer] Project functional region into white matter

n Wed, Dec 18, 2019 at 2:28 PM Greve, Douglas N.,Ph.D. > mailto:dgr...@mgh.harvard.edu>> wrote: > > Hi Corinna, if I understand correctly, you basically have cortical GM > ROIs in CVS space and you want to create an ROI of the adjacent > WM. Is > that right? How f

Re: [Freesurfer] Project functional region into white matter

Hi Corinna, if I understand correctly, you basically have cortical GM ROIs in CVS space and you want to create an ROI of the adjacent WM. Is that right? How far do you want to extend the ROI  into WM? Do you want to do something like a wmparc.mgz? doug On 12/18/19 9:55 AM, Corinna Bauer wrote:

Re: [Freesurfer] Manual segmentation to volume

in this case, I might try mri_vol2vol, something like mri_vol2vol --fstal 1 --interp nearest --mov example.mgz --s subject --regheader --o example.mni305.mgz That is a linear transform. If you want a non-linear, I can walk you through that too On 12/18/19 10:13 AM, Benjamin Ineichen wrote: > >

Re: [Freesurfer] Conversion fMRI volumes to surface

It is right if the register.dat maps 4d_inputBOLD.nii to the conformed subject anatomical space. You can check this with tkregisterfv --mov 4d_inputBOLD.nii' --reg 'register.dat' On 12/18/19 10:23 AM, Marina Fernández wrote: > > External Email - Use Caution > > Thank you Doug/Bruce. >

Re: [Freesurfer] Transform LIA orientation to RAS

I'm not sure what you mean. Surface data does not have an orientation in the way that a volume does On 12/18/19 10:29 AM, Marina Fernández wrote: > > External Email - Use Caution > > Dear Freesurfer experts, > > How can I transform an EPI-surface with LIA orientation to RAS >

Re: [Freesurfer] using different Freesurfer versions for cross-sectional & longitudinal processing

I think it should be ok in principle, though it might fail because the v6 long stream expects there to be certain files with certain names, and they might not be there with 5.1. On 12/16/2019 2:49 PM, Morgan Botdorf wrote: External Email - Use Caution Dear Freesurfer Experts, We have

Re: [Freesurfer] Conversion fMRI volumes to surface

Yes, use mri_vol2surf. Make sure to use --projfrac 0.5 to sample in the middle of cortex. Run it with --help to get examples. On 12/17/2019 11:16 AM, Marina Fernández wrote: External Email - Use Caution Dear experts, I’ve done the fMRI preprocessing and now I would like to convert each

Re: [Freesurfer] (no subject)

sforms/talairach.m3z $SUBJECTS_DIR/BN_Atlas_subcortex.gca $SUBJECTS_DIR/1122/mri/BN_Atlas_subcotex.mgz Best, Boris Am 16.12.2019 um 21:12 schrieb Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>>: There is something weird about that file. How was it created? doug ps. Please incl

Re: [Freesurfer] (no subject)

ad(/Users/boris/Desktop/MirLIND_test/1122/mri/N_Atlas_subcotex.mgz, > -1): could not open file > >> Am 16.12.2019 um 19:08 schrieb Greve, Douglas N.,Ph.D. >> mailto:dgr...@mgh.harvard.edu>>: >> >> mri_info N_Atlas_subcotex.mgz > > > _

Re: [Freesurfer] (no subject)

z: > -rwxrwxrwx 1 boris  staff  37013 13 Aug 23:30 BN_Atlas_subcotex.mgz > > Best, > Boris >> Am 13.12.2019 um 23:53 schrieb Greve, Douglas N.,Ph.D. >> mailto:dgr...@mgh.harvard.edu>>: >> >> pwd > > > _

Re: [Freesurfer] Pial surface does not follow the gray/csf boundary

It is hard to say. The 0.25mm may be throwing it off. You can try adding -r 0.25. This will increase the force that repels the pial surface from the white by a factor of 10. That might be enough. But there are a lot of places where mris_make_surfaces assumes that the voxels are 1mm. Sometimes

Re: [Freesurfer] Thickness problem

Can you try running the ROI results with mri_glmfit? ie, if you ran aparcstats2table to get the ROI results you input to SPSS, then run mri_glmfit --table table.dat --fsgd g1v4.fsgd --C group.diff.mtx --glmdir table.g1v4.glmdir where table.dat is the result of aparcstats2table Then look at

Re: [Freesurfer] (no subject)

AM Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> wrote: Are you running this from 1122/mri and is BN_Atlas_subcotex.mgz in that folder? On 12/12/19 12:57 PM, Boris Rauchmann wrote: > > External Email - Use Caution > > My-Computer:~ boris$ mri_aparc2aseg --s 112

Re: [Freesurfer] Study specific template

inclusion of voxels in these regions which could possibly explain why these might be outliers compared to the rest of the group. - Nandita On 12/12/19, 7:02 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Greve, Douglas N.,Ph.D."<mailto:fr

Re: [Freesurfer] Study specific template

in terms of > parcellation. Any pointers on how I can investigate and if a custom volume > template might help? > > Thanks, > Nandita > > > > On 12/5/19, 1:36 PM, "freesurfer-boun...@nmr.mgh.harvard.edu on behalf of > Greve, Douglas N.,Ph.D."

Re: [Freesurfer] (no subject)

aseg.mgz I get: ERROR: cannot find aseg >>> .../fs_all_subjects/xyz/mri/aseg.mgz >>> The file BN_Atlas_subcotex.mgz was created using: >>> mri_ca_label $SUBJECTS_DIR/xyz/mri/brain.mgz >>> $SUBJECTS_DIR/xyz/mri/transforms/talairach.m3z >>> $SUBJECTS_DIR/B

Re: [Freesurfer] flat maps in native space

ng > > Massachusetts General Hospital > > 149 13th Street, 149-2615 > > Charlestown, MA, USA, 02129 > > > > ------------ > *From:* freesurfer-boun...@nmr.mgh.harvard.edu > on behalf of Greve, Douglas

Re: [Freesurfer] Group analysis with gray matter volume in FS 6.0

When you say "gray matter volume", does it mean you are trying to do a VBM-style analysis? You can't do VBM with FS. You can do an analysis of cortical GM volume in a similar way. When you run mris_preproc, specify "volume" as the --meas On 12/12/19 12:58 PM, Marisa Cathryn Ross wrote: > >

Re: [Freesurfer] flat maps in native space

I'm not sure what is going on here, but I would guess that the v6 hires stream is not behaving  very well. I would suggest using a patch I created the HCP. If you are in the version 6 environment, you can run recon-all.v6.hires the same way you did recon-all, but do not use -hires and instead

Re: [Freesurfer] selxavg in native space vs fsaverage space

Hi Mona, not sure what you are trying to do. When you say "native" space, do you mean native functional space or native anatmical space?  If you want to analyze the data on the native surface, you can use --surf self when you run preproc-sess and mkanalysis-sess (instead of specifying

Re: [Freesurfer] (no subject)

running on it. > > Thanks, > Boris > > On Mon, Dec 2, 2019 at 5:31 PM Greve, Douglas N.,Ph.D. > mailto:dgr...@mgh.harvard.edu>> wrote: > > Can you send the log file for each of the gtmseg runs? > > On 11/26/2019 1:09 PM, Boris Rauchmann wrote: >>

Re: [Freesurfer] tkregisterfv problems

Try renaming the reg to something.lta On 12/10/2019 11:04 AM, Vicky Yang wrote: External Email - Use Caution Dear Freesurfer experts, I am using bbregister to register my functional template image into T1 image. The bbregister is running fine. But when I tried to view registration

Re: [Freesurfer] "Bad CPU type in executable" error

There is also tkregisterfv, which takes all the same arguments as tkregister2 but uses freeview instead On 12/9/19 1:39 PM, Hoopes, Andrew wrote: > Hi Abhi, > > The tkregister GUI built for v6 is no longer supported on modern macs since > it's a 32-bit program, which Catalina will not run. If

Re: [Freesurfer] Vertex-wise ROI extractions on the surface

You can create a mask of the ROI using mri_annotation2label using the --seg output. Then create a mask with mri_binarize --i seg.nii.gz --match MATCHVAL --o mask.nii.gz where MATCHVAL is the ID of your ROI from $FREESURFER_HOME/FreeSurferColorLUT.txt You can then use the fslmeants command below.

Re: [Freesurfer] fsaverage for externally preprocessed subjects.

On 12/7/19 5:42 PM, Alvarado,Luis R wrote: > > External Email - Use Caution > > Hi all, > > I have a couple of questions regarding fsaverage: > > 1. Is this file updated every time a new subject is process with > recon-all? > No, fsaverage will not be changed. > > 1. If I obtain

Re: [Freesurfer] PETSurfer individual atlas for subcortocal segmentation

r for me what to merge using xcerebralseg. Thanks a lot! On Mon, Nov 18, 2019 at 8:28 PM Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> wrote: It gets the subcortical from apas+head.mgz which gets created along the way by xcerebralseg. You can create your own with xcerebrals

Re: [Freesurfer] Study specific template

nmr.mgh.harvard.edu on behalf of > Greve, Douglas N.,Ph.D." dgr...@mgh.harvard.edu> wrote: > > USE CAUTION: External Message. > > See the REAME file here > > https://urldefense.proofpoint.com/v2/url?u=ftp-3A__surfer.nmr.mgh.harvard.edu_pub_dist_freesurfe

Re: [Freesurfer] negative SUVr using PETsurfer

ller than other > regions and is pretty similar on both hemispheres so we are not sure > what could be causing this. Any suggestions much appreciated. > Many thanks > > Paul > > On Mon, Dec 2, 2019 at 5:15 PM Greve, Douglas N.,Ph.D. > mailto:dgr...@mgh.harvard.edu>>

Re: [Freesurfer] T2 in recon-all: command to correct pial surfaces errors

The same one that you would use with the T1 stream, just make sure to include -T2pial On 12/5/19 5:04 AM, Steve Petersen wrote: > > External Email - Use Caution > > Dear Freesurfer experts, > > I used t2 image as input in subjects that have already been processed > without them

Re: [Freesurfer] Question on GLM - correlation

all I look like for the single voxel? > > > ------------ > *From:* Greve, Douglas N.,Ph.D. > *Sent:* Thursday, December 5, 2019 12:40 PM > *To:* Barletta, Valeria ; Freesurfer > support list > *Subject:* Re: [Freesurfer] Question on GL

Re: [Freesurfer] Using pre-segmented results

gt; Jordi > > On Thu, Nov 28, 2019 at 8:47 AM Jordi Huguet <mailto:jhugu...@gmail.com>> wrote: > > Great, just what I was looking for! > > Thanks Douglas, > Jordi > > On Wed, Nov 27, 2019, 19:47 Greve, Douglas N.,Ph.D. > mailto:dgr...@mgh.harvard

Re: [Freesurfer] Study specific template

See the REAME file here ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/ On 12/5/19 11:47 AM, Joshi, Nandita wrote: > > External Email - Use Caution > > Hello, > > I am trying to make a study specific template based on the > instructions at: >

Re: [Freesurfer] Question on GLM - correlation

t; Shall I include ficvf.mgh as a regressor (pvr) and use the Contrast  1 > 0 0   or shall I use a completely different method? > > Thanks, sorry for the long interaction... > ------------ > *From:* Greve, Douglas N.,Ph.D. >

Re: [Freesurfer] about label to surface

Use mri_label2label. Run it with --help to get examples On 12/4/19 1:58 AM, 于倩倩 wrote: > > External Email - Use Caution > > Dear Freesurfer Expert: > First, I got the lh.parsorbitalis.label according to the command: > mri_annotation2label --subject fsaverage --hemi lh --outdir >

Re: [Freesurfer] DWI to T1 registration accuracy with bbregister

Are you 100% sure that the DTI and the anatomical are the same subject? Also, please send the bbregister log file On 12/5/19 12:14 PM, VictorM - Gmail wrote: > External Email - Use Caution > > Hi Freesurfer experts, > > I have been trying to run a registration between my DWi data and

Re: [Freesurfer] Reporting Results in a three group analysis

it. If i wanted to constrain my post-hoc > to be within the cluster(s) from the main effect how would I go about > running this through mri_glmfit? Would I include the --mask > sig.cluster.mgh in the command for mri_glmfit and then aslo > mri_glmfit-sim? > > On Mon, Dec 2, 2019

Re: [Freesurfer] hippocampal subfields as masks for mri_segstats

Try using this instead lh.hippoAmygLabels-T1.v21.FSvoxelSpace.mgz On 12/4/19 5:09 PM, Marcel Heers wrote: > > External Email - Use Caution > > Dear all, (dear Eugenio), > > I would like to use hippocampal subfields as masks for mri_segstats to > retrieve intensity values. I am having

Re: [Freesurfer] MRI label 2 label issue

try setting your SUBJECTS_DIR to the full path instead of "./" On 12/4/19 2:48 PM, Rellick, Stephanie wrote: > > External Email - Use Caution > > Hello, > > I am having an issue with the mri_label2label command. > > What I did was mri merge of the BA4 a and p labels for each hemisphere >

Re: [Freesurfer] Converting labels drew by freeview to volumeError: coordinate mismatch

c.nii --invertmtx > > The problem: > sc.nii and T1.nii don't align, the ROI of superior colliculus are in > the wrong place. > > I would highly appreciate If you have any suggestions as the ways to > get superior colliculus' ROI or mask. > > > > At 20

Re: [Freesurfer] Freeview Question

ation)? > I just wanted to ask for a confirmation. > > Many thanks, > > Pilar > > >>> Message: 2 >>> Date: Mon, 2 Dec 2019 16:06:54 + >>> From: "Greve, Douglas N.,Ph.D." >>> Subject: Re: [Freesurfer] Fw: Regression Analysis accounting for

Re: [Freesurfer] surfaceholes in aseg.stats

Those are the number of defects in the ?h.orig.nofix. Not sure why the two people see different numbers. Are you totally sure they are being run in exactly the same way? If they made different edits (control points, brain mask) then it could result in different number of holes On 12/3/2019

Re: [Freesurfer] Multiple comparison using Monte Carlo

the cluster size p-value based on DOF (degree of freedom), like the t-ratios table including a DOF? Thanks a lot! I don't know what you mean. Best regards, Ting On Mon, Dec 2, 2019 at 1:59 PM Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> wrote: Correct. This is no different than, eg, a

Re: [Freesurfer] -qcache and thickness questions

e la part de Greve, Douglas N.,Ph.D. <mailto:dgr...@mgh.harvard.edu> Envoyé : mardi, 3 décembre 2019 02:14:08 À : freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> Objet : Re: [Freesurfer] -qcache and thickness questions On 12/2/2019 7:12 PM, Joëlle Ismay Ros

Re: [Freesurfer] topological defect error

Look at the lh.orig.nofix and see if you can find the defect. Also, look at it in the volume and the surface views. Might be cerebellum On 12/3/2019 11:30 AM, Laurel Quinlan wrote: External Email - Use Caution Hi Freesurfer Support, One of my colleagues receives the following error

Re: [Freesurfer] [External] Freesurfer Digest, Vol 190, Issue 3

orrecting for disease duration)? > I just wanted to ask for a confirmation. > > Many thanks, > > Pilar >> Message: 2 >> Date: Mon, 2 Dec 2019 16:06:54 + >> From: "Greve, Douglas N.,Ph.D." >> Subject: Re: [Freesurfer] Fw: Regression Analysis accounti

Re: [Freesurfer] -qcache and thickness questions

On 12/2/2019 7:12 PM, Joëlle Ismay Rosanne Van Der Molen wrote: External Email - Use Caution Dear Freesurfer experts, After running the -qcache option to extract thickness data for every subject, I tried pulling all the data together in order to get a matrix of subjects x vertices

Re: [Freesurfer] Reporting Results in a three group analysis

I don't think there is a standard way to do this. A vertex-wise analysis is not the same thing as a averaging over a group of vertices. I guess you could constrain your post-hoc analysis to be within the main effect cluster; that would be most consistent. But I don't think you'd have any

Re: [Freesurfer] negative SUVr using PETsurfer

It may or may not be something that needs to be fixed. The PVC is just a linear model where the regression coefficients are the uptake in each ROI. As with any model, it adjusts the regression coefs to minimize the error in the fit. If some end up being less than zero when you really expect all

Re: [Freesurfer] Multiple comparison using Monte Carlo

nothing to do with the analysis metrics that I have used. Do I understand correctly? Best regards, Ting Li On Mon, Dec 2, 2019 at 11:57 AM Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> wrote: On 12/2/2019 11:58 AM, Ting Li wrote: External Email - Use Caution Dear Dr. D

Re: [Freesurfer] Multiple comparison using Monte Carlo

ecord area of maximum cluster 6. Repeat over desired number of iterations (usually > 5000) Thank you so much! Best regards, Ting On Mon, Dec 2, 2019 at 10:20 AM Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> wrote: That will use the pre-computed ("cached") CSD files

Re: [Freesurfer] (no subject)

, 2019 at 8:28 PM Greve, Douglas N.,Ph.D. mailto:dgr...@mgh.harvard.edu>> wrote: It gets the subcortical from apas+head.mgz which gets created along the way by xcerebralseg. You can create your own with xcerebralseg by specifying your volume as the mergevol. I think this will work, but I'm no

Re: [Freesurfer] Multiple comparison using Monte Carlo

That will use the pre-computed ("cached") CSD files distributed with FreeSurfer. This used 10,000 iterations. On 12/1/2019 11:34 PM, Ting Li wrote: External Email - Use Caution Dear Freesurfer Expert: I have used the simulation code as show below: mri_glmfit-sim \ --glmdir

Re: [Freesurfer] Problems about registration and tksurfer

Try using mri_vol2surf to sample your fMRI onto the surface, then load it as a surface overlay in freeview On 11/29/2019 3:35 AM, 朱青 wrote: External Email - Use Caution Dear madam or sir, I'm a student in China who use the Freesurfer to analyse my fMRI data and overlay some

Re: [Freesurfer] about mri_vol2surf and mri_surf2surf

On 11/29/2019 4:27 AM, 于倩倩 wrote: External Email - Use Caution Hello, I have some questions about the command of mri_vol2surf and mri_surf2surf 1. For fMRI data, I find previous paper reported that they used standard SPM8 preprocessing routines, no normalize to standard MNI152

Re: [Freesurfer] fsfast no run directories

In the bold directory, it looks like you have one run directory called "1". Change this to "001" On 11/29/2019 1:48 AM, Renew Andrade wrote: External Email - Use Caution Dear FreeSurfer experts: I have some issues with "preproc-sess" because I cannot seem to get the setup of the

Re: [Freesurfer] Fw: Regression Analysis accounting for one variable

@nmr.mgh.harvard.edu/msg32860.html), but with only one group. How would you recommend to proceed? Many thanks, Pilar Message: 2 Date: Wed, 27 Nov 2019 16:56:20 + From: "Greve, Douglas N.,Ph.D." <mailto:dgr...@mgh.harvard.edu> Subject:

Re: [Freesurfer] Converting labels drew by freeview to volumeError: coordinate mismatch

! 发件人: Greve, Douglas N.,Ph.D.<mailto:dgr...@mgh.harvard.edu> 发送时间: 2019年11月28日 0:59 收件人: freesurfer@nmr.mgh.harvard.edu<mailto:freesurfer@nmr.mgh.harvard.edu> 主题: Re: [Freesurfer] Converting labels drew by freeview to volumeError: coordinate mismatch I'm not sure what the problem

Re: [Freesurfer] Using pre-segmented results

It might work if you mkdir -p FOO/mri cp yourwm.mgz FOO/mri/wm.mgz cp inputdata.mgz FOO/mri/orig/001.mgz then run recon-all -s FOO -all On 11/27/2019 12:39 PM, Jordi Huguet wrote: External Email - Use Caution Hi Bruce, Many thanks for your reply. I understand from your answer that it

Re: [Freesurfer] Applying -qcache following manual edits

yes, in fact, what you have done is the preferred method. Just run recon-all with -qcache instead of -all (or any other directive). Also note that qdec is not very flexible, so you may want to use the command line stream. On 11/27/2019 10:21 AM, Marisa Cathryn Ross wrote: External

Re: [Freesurfer] Converting labels drew by freeview to volume Error: coordinate mismatch

I'm not sure what the problem is. You say that they match when you load the T1 and the sc. If so, what is the problem? On 11/27/2019 7:57 AM, zorothustra wrote: External Email - Use Caution Hello Freesurfer Developers, I'm trying to get superior colliculus' ROI mannually by freeview.

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

www.neura.edu.au/help-research/subscribe> ________ From: "Greve, Douglas N.,Ph.D." <mailto:dgr...@mgh.harvard.edu> To: "Freesurfer support list" <mailto:freesurfer@nmr.mgh.harvard.edu>, "Kersten Diers, DZNE" <mailto:kerste

Re: [Freesurfer] PetSurfer questions

what ligand are you using? Do you expect it to be higher in GM and in WM? What are the values in the gtm.stats file relative to when you run it without PVC? How did you choose 5 as the --psf? On 11/26/2019 2:53 AM, Soo-Jong Kim wrote: External Email - Use Caution Dear FreeSurfer

Re: [Freesurfer] [recon-all] [use of -T2] Does only -autorecon3 use -T2?

Yes, the T2 is only used to refine the pial surface On 11/26/2019 5:14 PM, Billah, Tashrif wrote: Hi all, Is -T2 used only in -autorecon3 as shown here: recon-all -subject subjectname -T2 /path/to/T2_volume -T2pial -autorecon3 In

Re: [Freesurfer] extract lgi

yes, see https://surfer.nmr.mgh.harvard.edu/fswiki/LGI On 11/26/2019 2:07 AM, An Lijun wrote: External Email - Use Caution Dear Yanyan, Actually you could refer to the freesurfer tutorial firstly. Best Regards, An Lijun Lin Yanyan mailto:linyan...@outlook.com>> 于2019年11月26日周二

Re: [Freesurfer] How do I fix this white matter boundary issue?

Is the ventricle properly segmented in the aseg.presurf.mgz? If not, try running recon-all with -bigventricles On 11/22/2019 2:21 PM, Taylor, Lisa Marie wrote: External Email - Use Caution Hi there, I am working on a participant that has abnormally large ventricles. This has

Re: [Freesurfer] about to segmentation

not yet, but those are on our list On 11/22/2019 1:20 AM, Halil Aziz VELİOĞLU wrote: External Email - Use Caution Hi Mr/Mrs, I want to segment substantia nigra, nucleus ruber (red nucleus) and subthalamic nucleus in Freesurfer. These regions are not in aseg.stats file. So how can I

Re: [Freesurfer] Map fMRI data onto surface

> Also, I was just informed that the fMRI 4D series and the MRI are not > scanned in the same day. Is it possible to register them in freesurfer. > > Many thanks. > > Best, > An > image.png > > > Greve, Douglas N.,Ph.D. <mailto:dgr...@mgh.harvard.edu>> 于20

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

> Message: 4 > Date: Wed, 20 Nov 2019 22:45:18 + > From: "Greve, Douglas N.,Ph.D." <mailto:dgr...@mgh.harvard.edu>> > Subject: Re: [Freesurfer] Question about the input for longitudinal >         processing pipeline > To:

Re: [Freesurfer] Map fMRI data onto surface

gt; The log file is also attached to this email, please take a look at > your convenience. > > Many thanks. > > Best, > An > > image.png image.png > > Greve, Douglas N.,Ph.D. <mailto:dgr...@mgh.harvard.edu>> 于2019年11月21日周四 下午2:49写道： > > It is hard to

Re: [Freesurfer] Map fMRI data onto surface

e registered image after step2. It looks like they > are not perfectly aligned. Is there anyway to improve that and also > the final result? > > Many thanks. > > Best, > An > image.png > > Greve, Douglas N.,Ph.D. <mailto:dgr...@mgh.harvard.edu>> 于2019年11月21日

Re: [Freesurfer] Recon-all Error

ization/denoising for 3T scanners. I > haven’t had a chance to look deeper into it. Please let me know what > you think about it? > > Thank you! > Meena > > On Wed, Nov 20, 2019 at 5:51 PM Greve, Douglas N.,Ph.D. > mailto:dgr...@mgh.harvard.edu>> wrote: > &

Re: [Freesurfer] Map fMRI data onto surface

35% sounds high to me. Did you actually check the registration You can always load the the fMRI as an overlay in freeview, try tksurferfv subject lh inflated -ov fmri-sampled-on-lh.mgz Also, please include command lines you used On 11/21/19 10:03 AM, An wrote: > > External Email - Use

Re: [Freesurfer] Substantia nigra delineation

Sorry, we don't have tools to segment substantia nigra. Hopefully coming soon On 11/21/19 4:34 AM, Aline Delva wrote: > > External Email - Use Caution > > Dear, > > We would like to delineate the substantia nigra using a 3D Sag BRAVO > and a 3D Sag FLAIR in freesurfer. > > What is the

Re: [Freesurfer] Freesurfer analyses in MATLAB

sorry, I don't know what it is you are doing here. what are beta2 and X2? what is DV? what are you plotting against what? On 11/14/19 3:25 PM, cody samth wrote: > > External Email - Use Caution > > Hi I'm interested in running some analyses in matlab using freesurfer > commands. I'm

Re: [Freesurfer] mask for cortical thickness

Pass the mask you want to mri_glmfit with either --label or --mask (depending on your format). You can convert the aparc to labels using mri_annotation2label , then pick the label you want. In this case, you cannot use --cache as that has been computed using whole hemi. You can generate your

Re: [Freesurfer] Recon-all Error

This is something that is being triggered by use -3T. Is there a reason you are using that option? On 11/19/19 5:15 PM, Meena M. Makary wrote: > > External Email - Use Caution > > Hi, > > I have been getting this error with one of my subjects Recon-all. I am > attaching the recon-all

Re: [Freesurfer] Local Gyrification Index: freesurfer version

It has not changed (and is no longer supported) On 11/19/19 6:48 AM, Steve Petersen wrote: > > External Email - Use Caution > > Dear Freesurfer experts, > > What freesurfer version do you recommend to perform the local > gyrification index, version 6 or 6 development version? > > >

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

e those images as inputs in the longitudinal pipeline? And the same > question for mp2rage images, are they OK to use as well, or are they > not suitable for this pipeline? > Best, > Darko > > > -- > > Message: 11 > Date: Mon, 18 Nov 2

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

I responded to this a few days ago. Below is what I said 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

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

yes On 11/18/19 8:59 PM, An Lijun wrote: > > External Email - Use Caution > > Thanks for your reply! > You mean LeftCerebralCortex is actually lhCortex in aseg.stats, right? > > Best Regards, > An Lijun > > > Greve, Douglas N.,Ph.D. <mailto:dgr...@mgh.

Re: [Freesurfer] 4D multi-frame parcellation

why did you call it bert? It just makes things confusing On 11/18/19 2:53 PM, An wrote: > > External Email - Use Caution > > Here is my recon-all command line: > recon-all -i ana_Vol.nii -s bert -all > Many thanks. > > Best, > An > > >

Re: [Freesurfer] 4D multi-frame parcellation

e. I ran 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

Re: [Freesurfer] (no subject)

.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 at 5:10 PM Greve, Douglas

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

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

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