[Freesurfer] mris_pmake update

? Thanks Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il ___ Freesurfer mailing list Freesurfer

Re: [Freesurfer] mris_pmake update

Thank you! I have Ubuntu 14.04.1 LTS, 64 bit. Best Francesca 2015-01-08 16:45 GMT+02:00 Rudolph Pienaar : > I can send you the updated binary. What Linux are you running on? > CentOS? 32 bit? 64 bit? > > Best > -=R > > On 1/8/15 09:23 , Francesca Strappini wrote: > &

[Freesurfer] mris_convert converting annot to gifti format

ce for the help! Best Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il ___ Freesurfer mailing list

[Freesurfer] mris_convert gifti

Hi, sorry to bother, I'm re-posting this question just in case it got lost. Thanks. Hi, I have a question about mris_convert. I've created some regions on the surface and now I would like to make them directly readable into SUMA. I ran this command but it ended with an error message. mris_conver

Re: [Freesurfer] mris_convert gifti

lman/listinfo/freesurfer > > > The information in this e-mail is intended only for the person to whom it > is > addressed. If you believe this e-mail was sent to you in error and the > e-mail > contains patient information, please contact the Partners Compliance > HelpLine

Re: [Freesurfer] mris_convert gifti

Thank you! Do you know which function should I use? Best Francesca 2015-05-05 15:30 GMT+03:00 Bruce Fischl : > yes, you can use a label for this (we use the ?h.cortex.label for this > purpose routinely to remove non-cortical stuff) > > On Tue, 5 May 2015, Francesca Strappini wrote

Re: [Freesurfer] mris_convert gifti

+03:00 Francesca Strappini : > Thank you! Do you know which function should I use? > > Best > Francesca > > 2015-05-05 15:30 GMT+03:00 Bruce Fischl : > >> yes, you can use a label for this (we use the ?h.cortex.label for this >> purpose routinely to remove non-co

Re: [Freesurfer] mris_convert gifti

st of vertexes related to the region and not all the surface vertexes. Thanks for the help! Francesca 2015-05-05 23:04 GMT+02:00 Bruce Fischl : > you can just create a label file I guess. What input does SUMA take? > > On Tue, 5 May 2015, Francesca Strappini wrote: > > Sorry, just

Re: [Freesurfer] mris_convert gifti

Matt. > > On 5/5/15, 5:30 PM, "Bruce Fischl" wrote: > > >sorry, I think this may be a question for the SUMA people - I don't know > >what .dset format is. Are you going to do the masking within SUMA? I'll > >cc > >Ziad so he can chime

Re: [Freesurfer] mris_convert gifti

wrote: > > > sorry, I think this may be a question for the SUMA people - I don't know > what .dset format is. Are you going to do the masking within SUMA? I'll cc > Ziad so he can chime in. > > > > cheers > > Bruce > > > > On Tue, 5 May 2015

[Freesurfer] selxavg3-sess error with phase-encoded data

tached the Xtmp.mat file from the output folder in case is needed. Thank you! Best Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il Xtmp.mat D

[Freesurfer] selxavg3-sess error

d(A); Error in fast_selxavg3 (line 279) XCond = cond(XtX); Thanks! Best Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...

Re: [Freesurfer] selxavg3-sess error

Hi Doug, it looks like my email with attached the Xtmp.mat file didn't arrive. How can I send it to you? Thanks! Francesca 2016-06-08 15:44 GMT+02:00 Douglas Greve : > Do you have both polar and eccen data? If so, can you send the Xtmp.mat > file? > > > On 6/8/16 6:08 AM,

Re: [Freesurfer] selxavg3-sess error

it won't make much difference. > > On 06/08/2016 09:55 AM, Francesca Strappini wrote: > > I have only something similar in the temporal dynamics to the > > eccentricity data. I attached the Xtmp.mat file. > > Thank you! > > > > Francesca >

[Freesurfer] retinotopy analysis documentation

Hello Freesurfers, Where can I find the documentation about how is the retinotopic analysis performed in Freesurfer? Thanks. Best Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail

[Freesurfer] retinotopy analysis documentation

Hello Freesurfers, I'm re-posting this question. Where can I find any documentation about how is the retinotopic analysis performed in Freesurfer? Thanks. Best -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israe

[Freesurfer] retinotopic analysis

Hello Freesurfers, Where can I find any documentation about how is retinotopic analysis performed in Freesurfer? Thanks. Best -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail

Re: [Freesurfer] V3A ROI?

t; http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institu

[Freesurfer] Coomand not found

Hi, I'm just starting out with freesurfer. I downloaded CentOS6_x86_64 and I have Ubuntu 12.04 LTS. I have set up the licence file and configured freesurfer: tcsh setenv FREESURFER_HOME /media/Shared_Data/freesurfer source $FREESURFER_HOME/SetUpFreeSurfer.csh freesurfer-Linux-centos6_x86

[Freesurfer] converting labels to MNI space

ii.gz Thanks for your help, Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il ___ Freesurfer mailing

Re: [Freesurfer] converting labels to MNI space

ng, does it? Also, you might have better > alignment if you run recon-all on the mni152 brain, then use > mri_label2label to map the label from the individual into the 152 space > using the surface transform, then convert that to the volume. > > On 11/30/2015 10:13 AM, Francesca

Re: [Freesurfer] converting labels to MNI space

> > > On 12/3/15 8:46 AM, Francesca Strappini wrote: > > Thank you! > > I run the recon-all on the MNI brain and now the first step, label2label, > produced a label which is perfectly mapped on the surface of the MNI > template. > I tried to run the second step, map

Re: [Freesurfer] converting labels to MNI space

; LabelRead failed > > freeview.bin: empty label > > > > 2015-12-03 16:57 GMT+02:00 Douglas Greve > <mailto:gr...@nmr.mgh.harvard.edu>>: > > > > Use --regheader /usr/share/fsl/data/standard/MNI152_T1_2mm.nii.gz > > instead of --identity > > > > >

[Freesurfer] mri_vol2surf misaligment

t --o Katkov_OT_45_LH.nii.gz I used as registration matrix the one produced by the preprocessing step but when I try to visualize the map on the surface it looks like completely misaligned. Thank you Best Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl S

[Freesurfer] surface-based spatial smoothing model

Hi all, I would like to know which model has been implemented for the surface-based spatial smoothing in Freesurfer (for example in mri_vol2surf). Heat kernel smoothing and/or diffusion smoothing? Thank you Best Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann

Re: [Freesurfer] surface-based spatial smoothing model

rface-based Gaussian. > > cheers > Bruce > > > On Tue, 3 May 2016, Francesca Strappini wrote: > > > Hi all, > > > > I would like to know which model has been implemented for the > surface-based > > spatial smoothing in Freesurfer (for example in m

Re: [Freesurfer] surface-based spatial smoothing model

t; > http://www.ncbi.nlm.nih.gov/pubmed/?term=Sereno%20MI%5BAuthor%5D&cauthor=true&cauthor_uid=17011792 > >. > > > > On 05/03/2016 09:03 AM, Francesca Strappini wrote: > > Thank you! > > Is there a paper I can read as a reference? > > > > 2016-05-03 15:

[Freesurfer] niiRead error

could not read movierestTest.nii.gz as type 24 Thanks Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.

Re: [Freesurfer] niiRead error

Fischl wrote: > > Hi Francesca > > > > why is the nifti 5-dimensional? The code is complaining that it doesn't > > know how to intepret the input volume > > > > cheers > > Bruce > > On Sun, 30 Jul 2017, Francesca > > Strappini wrote: > >

Re: [Freesurfer] niiRead error

It does work with 6.0, thank you! 2017-07-31 20:59 GMT+03:00 Douglas Greve : > I think this may be fixed in 6.0 > > On 7/31/17 12:43 PM, Francesca Strappini wrote: > > Thanks for the reply. > > freesurfer-Linux-centos6_x86_64-stable-pub-v5.3.0. > > I opened it with

[Freesurfer] make_average_subject monkey data

ORS at Tue Mar 13 20:26:58 CET 2018 To report a problem, see http://surfer.nmr.mgh.harvard.edu/fswiki/BugReporting -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weiz

Re: [Freesurfer] make_average_subject monkey data

las N. Greve : > I don't know what is going on there except that the average surfaces are > probably wrong in some way. It looks like it made it all the way through > except for that step, so all of the output should be there. How does it > look? > > > On 03/13/2018 05:2

Re: [Freesurfer] make_average_subject monkey data

+01:00 Douglas N. Greve : > Check the talairach.xfm registration. It is probably way off. It does > not have to be perfect (esp since they are different species), but the > two subjects should have a similar registration > > > On 03/14/2018 07:27 PM, Francesca Strappini wrote

Re: [Freesurfer] make_average_subject monkey data

cd subject/mri/transforms > > tkregister --mov ../nu.mgz --s fsaverage --reg talairach.lta > > If so, you can try running make_average_subject with --xform talairach.lta > > I've never done this, but it might work :) > > > > On 03/15/2018 01:02 PM, Francesca Strappini

Re: [Freesurfer] make_average_subject monkey data

; > 2. Convert the lta to an xfm: > > tkregister --mov ../orig.mgz --lta talairach.lta --reg deleteme.reg.dat > --xfmout talairach.xfm --s fsaverage --surfs --noedit > > 3. rerun make_average_subject > > On 3/16/18 5:24 AM, Francesca Strappini wrote: > > Thanks Doug! &g

[Freesurfer] freesurfer selxavg3-sess error

mize(flac0); >> -- ERROR: fast_selxavg3() failed\n Thank you! Best Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@we

Re: [Freesurfer] freesurfer selxavg3-sess error

-- ERROR: fast_selxavg3() failed\n 2018-04-24 20:27 GMT+03:00 Douglas Greve : > Try deleting the contrasts (.mat files) and rerunning > > On 4/24/18 5:48 AM, Francesca Strappini wrote: > > > Dear FreeSurfer experts, > > I'm trying to analyze some

Re: [Freesurfer] freesurfer selxavg3-sess error

External Email - Use Caution Hi, sorry, maybe my last email got lost. Is there anything I can try to fix this problem with selxavg3-sess? Thanks! Best Francesca 2018-04-24 20:35 GMT+03:00 Francesca Strappini : > Thank you for the reply! > I deleted the contrasts and ru

Re: [Freesurfer] Coomand not found

. > -Louis > > On Sat, 10 May 2014, Francesca Strappini wrote: > >> Hi, I'm just starting out with freesurfer. I downloaded CentOS6_x86_64 >> and I have Ubuntu 12.04 LTS. I have set up the licence file and >> configured freesurfer: >> >> tcsh &

Re: [Freesurfer] Coomand not found

t found shalim-ubunut:/media/Shared_Data/freesurfer/bin> ls -la tkmedit -rwxrwxrwx 1 francesca francesca 102 May 14 2013 tkmedit 2014-05-12 18:52 GMT+03:00 Louis Nicholas Vinke : > Ok, could you send the entire terminal output? > Thanks. > -Louis > > On Mon, 12 May 2014, Francesca S

Re: [Freesurfer] Coomand not found

>> -rwxrwxrwx 1 francesca francesca 102 May 14 2013 tkmedit >> >> 2014-05-12 18:52 GMT+03:00 Louis Nicholas Vinke < vi...@nmr.mgh.harvard.edu>: >>> Ok, could you send the entire terminal output? >>> Thanks. >>> -Louis >>> >>> On M

Re: [Freesurfer] Coomand not found

up via: > sudo chgrp -R groupname * > > where groupname is the new group. > > If you want to give world read/execute permissions do this: > cd $FREESURFER_HOME > sudo chmod -R a+rX * > > > Best, Martin > > > On 05/14/2014 04:16 AM, Francesca Strappini wrote: >

Re: [Freesurfer] Coomand not found

gt; > D > > On Wed, May 14, 2014 at 9:51 AM, Francesca Strappini > wrote: > > Ok, thank you! > > > > I sourced freesurfer and then I tried: > > cd $FREESURFER_HOME > > sudo chmod -R a+rX * > > > > But I still get the same error: > >

Re: [Freesurfer] Coomand not found

> directory, but it would take a lot of digging to figure out how) to > install it on the pure linux partition. > > HTH, > D > > On Wed, May 14, 2014 at 10:18 AM, Francesca Strappini > wrote: > > Yes, it's a dual boot system (Windows7 and Ubuntu 12.04 LTS) > >

[Freesurfer] selxavg3-sess error

Dear all, I've run selxavg3-sess and I got this error message when it tried to read the fmcsm file (fmc.sm5.DM.lh.nii.gz). Thank you for your help, Francesca shalim-ubuntu:/usr/local/freesurfer/fsfast/MeytalRetinotopy> selxavg3-sess -a rtopy.DM.lh -s SUBJ01 Surface data DM lh --

Re: [Freesurfer] fieldsign map display

Yes, this was the command line fieldsign-sess -a rtopy.LG.lh -s SUBJ02 -patch lh.full.flat.patch.3d -fwhm 0 Thanks! Francesca 2014-09-04 15:52 GMT+03:00 SHAHIN NASR : > Hi, > Have you ran fieldsign-sess after your selxavg3-sess? > > > On Thu, Sep 4, 2014 at 8:35 AM, Fran

Re: [Freesurfer] selxavg3-sess error

oug > > On 8/28/14 9:49 AM, Francesca Strappini wrote: >> Dear all, >> >> I've run selxavg3-sess and I got this error message when it tried to >> read the fmcsm file (fmc.sm5.DM.lh.nii.gz). >> >> Thank you for your help, >> Francesca >> &

[Freesurfer] error with fast_selxavg3

/local/freesurfer/fsfast/MeytalRetinotopySmoothed/SUBJ09/bold/rtopy.HS.rh/Xtmp.mat Error using svd Input to SVD must not contain NaN or Inf. Error in cond (line 36) s = svd(A); Error in fast_selxavg3 (line 279) XCond = cond(XtX); -- Francesca Strappini, Ph.D. Neurobiology Department Weiz

Re: [Freesurfer] error with fast_selxavg3

t was not in the > parfile. Do you only have eccen for this or do you also have polar? > doug > > > On 11/08/2014 11:25 AM, Francesca Strappini wrote: > > Hi, I attached the file, thank you! > > > > Best > > Francesca > > > > 2014-11-06 18:58 GMT+0

[Freesurfer] selxavg3-sess contrasts error

flac0); >> -- ERROR: fast_selxavg3() failed\n Thank you! -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il ___

Re: [Freesurfer] selxavg3-sess contrasts error

). Check the paradigm file for this subject and run. > > On 08/22/2018 10:16 AM, Francesca Strappini wrote: > > > > External Email - Use Caution > > > > Hi, > > > > I'm trying to analyze a block-design experiment. I run selxavg3-sess: >

Re: [Freesurfer] freesurfer selxavg3-sess error

t; > > On 05/02/2018 10:06 AM, Francesca Strappini wrote: > > Hi, sorry, maybe my last email got lost. Is there anything I can try > > to fix this problem with selxavg3-sess? > > > > Thanks! > > Best > > Francesca > > > > 2018-04-24 2

Re: [Freesurfer] freesurfer selxavg3-sess error

External Email - Use Caution Thank you! I changed the event file and re-run the analysis. I got an error message when creating the contrast: mkanalysis-sess -analysis FF-MonkeyCassis-event.sm03.lh -surface MonkeyCassis lh -fwhm 3 -fsd bold -per-run -event-related -paradigm FF.par

[Freesurfer] partial FoV - registration failure

after? Thanks -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E-mail: francesca.strapp...@weizmann.ac.il ___ Freesurfer mailing list Freesurfer

Re: [Freesurfer] partial FoV - registration failure

in the session folder called anatomical/001 and put the anatomical in > there (eg, anat.nii.gz), then use -bbr-int anatomical anat > > > On 11/26/2018 02:58 PM, Francesca Strappini wrote: > > > > External Email - Use Caution > > > > Dear freesurfer experts

[Freesurfer] mri_segstat: same output with two different label

Index SegId NVertices Area_mm2 StructName Mean StdDev Min Max Range SNR 1 0161272 106116.2 Seg-0.9503 2.4005 -13.2314 11.430224.6617-0.3959 2 1 1369 871.1 Seg0001 1.3153 3.8989-8.2296 10.366618.5962 0.3373 Thanks a lot for the hel

Re: [Freesurfer] mri_segstat: same output with two different label

an you run your two > mri_segment commands and send me the terminal output of each? > As for the two mean intensity values, one (Seg0001) is from inside your > ROI and the other (Seg) is outside. You can have it exclude Seg > with --excludeid 0 > > > On 1/20/19 10:00 A

[Freesurfer] registration and resampling in native space

ke to resample the data based on the register.dat without upsampling and keeping the same FoV (3x3x3 mm; 64 64 50). Is it doable? Thanks! Best -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel Tel.: +972 58 444 2584 E

Re: [Freesurfer] registration and resampling in native space

ol2vol. It just changes the > header, so I think should do what you want. > > cheers > Bruce > > > On Tue, 12 Feb 2019, Francesca Strappini wrote: > > > > > External Email - Use Caution > > > > Dear Freesurfer's experts, > > > > I

Re: [Freesurfer] mri_segstat: same output with two different label

hing > wrong. Double check that your contrasts are correct. > > > On 2/10/19 9:47 AM, Francesca Strappini wrote: > > > > External Email - Use Caution > > > > Thanks a lot for the reply! > > If I run mri_diff order/z.nii.gz disorder/z.nii.gz I indeed get zer

Re: [Freesurfer] partial FoV - registration failure

scans where you have both the partial FoV and a whole > brain, you might be able to get an init reg by registering the partial > FoVs from different days. > good luck > > > > On 11/26/2018 03:19 PM, Francesca Strappini wrote: > > > > External Email - Use Cauti

Re: [Freesurfer] registration and resampling in native space

schl < fis...@nmr.mgh.harvard.edu> ha scritto: > Hi Francesca > > sorry, I defer to Doug on the details of mri_vol2vol. > > cheers > Bruce > > On Tue, 12 Feb 2019, > Francesca Strappini wrote: > > > > > External Email - Use Caution > &g

Re: [Freesurfer] registration and resampling in native space

an? If so, wouldn't be T2 weighted? If so, > you should use --t2 instead of --t1 in bbregister > > On 2/14/19 2:18 PM, Francesca Strappini wrote: > > > > External Email - Use Caution > > > > Hi Doug, > > > > Could you advise me about how to cor

Re: [Freesurfer] registration and resampling in native space

d us an image that shows why you think it can be improved? > > cheers > Bruce > On > Mon, 18 Feb 2019, Francesca Strappini wrote: > > > > > External Email - Use Caution > > > > Thank you!Now the registration is better but still not perfect. Is there >

Re: [Freesurfer] registration and resampling in native space

s to a single > template but otherwise keep everything in the functional space > > On 2/20/19 11:53 AM, Francesca Strappini wrote: > > > > External Email - Use Caution > > > > I'll try to find some visual way to show what I mean, but it's really > &

Re: [Freesurfer] registration and resampling in native space

.lta. Use that > with mri_label2vol passing your segmentation in with --seg. Run with --help > to get more info > > On 2/21/19 11:54 AM, Francesca Strappini wrote: > > External Email - Use Caution > Thanks a lot! > Running preproc-sess with the --per-session flag is

Re: [Freesurfer] registration and resampling in native space

t; conformed anatomical space? Use mri_info can compare the output > (particularly the vox2ras matrix) against orig.mgz. If they are the same, > you can try adding --invertmtx to the mri_label2vol command line. > > On 2/22/19 2:24 PM, Francesca Strappini wrote: > > External Emai

Re: [Freesurfer] registration and resampling in native space

the ROIs into the anatomical space or compute > a new registration to the space of the ROIs from the functional template > > On 2/22/19 3:43 PM, Francesca Strappini wrote: > > External Email - Use Caution > Thanks! > The vox2ras matrices are not same. > > T

Re: [Freesurfer] registration and resampling in native space

External Email - Use Caution Hi Doug, Sorry to bother, maybe my last message got lost. Do you think you can advice me on this type of registration? Thanks! Best Francesca On Fri, Feb 22, 2019, 11:44 PM Francesca Strappini < francescastrapp...@gmail.com> wrote: > Wh

[Freesurfer] mkanalysis-sess with a customized HRF

External Email - Use Caution Dear Freesurfer's experts, I would like to use a customized HRF with mkanalysis-sess. Is there a way to do it? Thanks! Best Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Re

[Freesurfer] full flat patch issue

Hi, I'm trying to create a full flat map. The process of flattening seems has finished without any errors, but I got this error message when I tried to show up the full flat patch: lh.full.flat.patch.3d: face[0] = 0, but face 0 not in vertex 0 face list Thanks a lot Francesca ___

[Freesurfer] register data to the surface

Hi! I successfully run the preprocessing on some polarangle data (preproc-sess -sf seesid -surface self lhrh -fwhm 5). Now I would like to do the subtraction between some runs and then to visualize this subtraction on the surface (so without to analyze the data with Fourier analysis). Does anybody

Re: [Freesurfer] register data to the surface

Sorry, I try to be more specific. I would like to be able to take the volume-to-surface transformation calculated on one set of functional data, and apply that transformation to another set of functional data (the subtraction) of the same subject. This will allow me to display arbitrary functional

Re: [Freesurfer] register data to the surface

Thanks a lot! I tried the registration with bbregister but unfortunately when I checked the result the functional volume was very distant from the target. Could I tried something else to improve the registration? I typed: bbregister --s subject --mov name_file.nii --reg register.dat --init-fsl --

[Freesurfer] license error

new one from the following page: http://surfer.nmr.mgh.harvard.edu/registration.html -- -- Error ConvertSurface (SUMA_ConvertSurface.c:589): if_name lh.pial.asc not found. failure: could not create surface lh.pial.gii --> is your FreeSurfer license installed?

[Freesurfer] monkey atlas D99

each functional run using the ROIs contained in the segmentation as masks. I suppose I should mri_segstats but I'm not sure how. Any suggestion? Thank you Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Weizmann Institute of Science 234 Herzl Street, Rehovot 7610001 Israel

Re: [Freesurfer] monkey atlas D99 {Disarmed}

l giorno lun 30 nov 2020 alle ore 00:03 Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> ha scritto: > Use mri_label2vol to map the segmentation into the fMRI space, then use > mri_segstats using the --avgwf option to get time courses. Run it with > --help to get examples > >

Re: [Freesurfer] monkey atlas D99 {Disarmed}

n Wed, Dec 23, 2020, 19:05 Greve, Douglas N.,Ph.D. wrote: > The argument to the --label flag should be a freesurfer label file, this > is a text file not an nii.gz file. > > On 12/21/2020 10:52 AM, Francesca Strappini wrote: > > External Email - Use Caution > Thank

[Freesurfer] monkey atlas resampling

sfast/ Monkeys/MonkeyCassis-FF-event-sm03-AVGmonkey/bold/template.nii.gz --o D99_registered2func.nii.gz However, the registration was completely lost and I had to register it again manually. Maybe I did something wrong? Thanks. Francesca -- Francesca Strappini, Ph.D. Neurobiology Department Wei

[Freesurfer] Cutting the Full Surface

External Email - Use Caution Dear FreeSurfer experts, I'm trying to cut and flatten the full surface. I understand that tksurfer is deprecated and on my PC does not work properly. Is there an alternative way to perform the cuts? Thank you, Francesca -- Francesca Stra

Re: [Freesurfer] Cutting the Full Surface

then hit "Fill Uncut Area", then > save as a patch > > > On 3/7/2022 12:03 PM, Francesca Strappini wrote: > > External Email - Use Caution > Dear FreeSurfer experts, > > I'm trying to cut and flatten the full surface. I understand that tksurfer > is

[Freesurfer] how to load flat surface in freeview

ommand line but nothing happened: [francesca@GIOVE surf]$freeview -f lh.inflated:patch=lh.full.flat.patch.3d Thank you, Francesca -- Francesca Strappini, Ph.D. Psychology Department Sapienza University of Rome Via dei Marsi 78, Rome 00185 Italy Tel.: +39 392 151 4029 E-mail: francesca.strapp...@

Re: [Freesurfer] how to load flat surface in freeview

b01_mprage/surf/lh.inflated > > > On 3/10/2022 7:32 AM, Francesca Strappini wrote: > > External Email - Use Caution > Dear Freesurfer experts, > > I'm trying to load the flat surface that I created with this command line: > > mris_flatten -w 10 lh.full.patch.3d l

[Freesurfer] retinotopy: MGH vs UCSD

Hi all, I would ask you about freesurfer and retinotopy. I'm going to begin the analysis of some retinotopic data. I would ask if you know if the retinotopic analysis made by MGH freesurfer is qualitatively comparable to, or it's good as, that made by USCD freesurfer (old freesurfer). Thank you kin

Re: [Freesurfer] retinotopy: MGH vs UCSD

old freesurfer, or csurf, is this: http://kamares.ucsd.edu/~sereno/csurf/tarballs/ made by Marty Sereno ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The information in this e-mai

[Freesurfer] anatomical ROI

Hi all, I would ask you about anatomical ROIs. I'm going to begin the analysis of some retinotopic data, my question is: when I draw the closed contours, does automatically my ROI contain the entire inner surface or just the outline? Thank you kindly in advance. Francesca ___