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

2019-11-13 Thread Bruce Fischl
Hi Dalton you need to give us a lot more information. What command did you run? What was the full output? cheers Bruce On Wed, 13 Nov 2019, Dalton Bermudez wrote: External Email - Use Caution -- Forwarded message - From: Dalton Bermudez Date: Wed, Nov

Re: [Freesurfer] Recon all hard failure,

2019-11-12 Thread Bruce Fischl
> > From: "Greve, Douglas N.,Ph.D." > To: "freesurfer" > Sent: Tuesday, November 12, 2019 4:46:49 PM > Subject: Re: [Freesurfer] Recon all hard failure, > > And before that you should check the orig and white surfaces > > On 11/12/2019 9:37

Re: [Freesurfer] Recon all hard failure,

2019-11-12 Thread Bruce Fischl
Hi Vicente I'm not sure what the images are showing - maybe the inflated surface? That isn't useful to look at in the volume. You should check the inflated.nofix surface and see if something big is wrong (cerebellum or skull attached, that kind of thing). There is a tutorial on our wiki for

Re: [Freesurfer] Version 5.3 vs. Version 6

2019-11-08 Thread Bruce Fischl
Hi Larissa I think we need more details. What do you mean you used 6 for anatomical ROI analysis? On the same subjects? Did you rerun them? Sorry, I can't figure out exactly what you are doing cheers Bruce On Fri, 8 Nov 2019, Larissa Bechtle wrote: >External Email - Use Caution > >

Re: [Freesurfer] Inconsistent Morphology Output

2019-11-08 Thread Bruce Fischl
or start by sending us the recon-all.log from the two runs On Fri, 8 Nov 2019, Chen, Christine wrote: External Email - Use Caution Hello,   My lab has been running T1 (MPRAGE) data through run_subject (uses recon-all, autorecon, mris_volume and mris_wm_volume) then

Re: [Freesurfer] Inconsistent Morphology Output

2019-11-08 Thread Bruce Fischl
Hi Christine maybe you can tar and gzip a subject that has been run twice with different results and file drop it or ftp it to us? cheers Bruce On Fri, 8 Nov 2019, Chen, Christine wrote: External Email - Use Caution Hello,   My lab has been running T1 (MPRAGE) data

Re: [Freesurfer] flat maps in native space

2019-11-08 Thread Bruce Fischl
Hi Mona that is pretty strange looking. Is the data somewhere local that we can take a look at it? I would guess that one of the cuts left a connection around, but would need to look at it to tell. Have you flattened other subjects successfully? cheers Bruce On Fri, 8 Nov 2019,

Re: [Freesurfer] recon-all -s SOME_SUBJECT exited with ERRORS

2019-11-07 Thread Bruce Fischl
>> On Thu, Nov 7, 2019 at 4:41 PM Bruce Fischl >> wrote: >> hmmm, does it always happen for this subject? What if you don't use >> -parallel? >> On Thu, 7 Nov 2019, Emanuel Alvaredo wrote: >> >> > >> > External Email - Use Caution

Re: [Freesurfer] recon-all -s SOME_SUBJECT exited with ERRORS

2019-11-07 Thread Bruce Fischl
why. Thanks in advance Emanuel On Wed, Oct 30, 2019 at 10:51 AM Bruce Fischl wrote: Hi Emanuel can you give us more details. What was your command line? What was the full job output? What is in the recon-all.log? Does this happen if you run directly instead of through

Re: [Freesurfer] Help with "orig.mgz"

2019-11-07 Thread Bruce Fischl
Hi Fernando it is a volume after resampling to 1mm isotropic, 8 bits/voxel and 256^3 cheers Bruce On Thu, 7 Nov 2019, Fernando Castellano wrote: External Email - Use Caution good afternoon, I am using freesurfer for my thesis in image technician. I would like to know

Re: [Freesurfer] Using individual FreeSurfer utilities without the whole package

2019-11-04 Thread Bruce Fischl
Hi Mike our license lets you do pretty much whatever you want :). That said, the recon pipeline is complex and it isn't so easy to pick and choose steps, although I guess if you are just processing already datasets that have already been run through recon-all it should be pretty

Re: [Freesurfer] recon-all -s SOME_SUBJECT exited with ERRORS

2019-10-30 Thread Bruce Fischl
Hi Emanuel can you give us more details. What was your command line? What was the full job output? What is in the recon-all.log? Does this happen if you run directly instead of through some type of batch server? cheers Bruce On Wed, 30 Oct 2019, Emanuel Alvaredo wrote: External

Re: [Freesurfer] FreeSurfer transforms

2019-10-20 Thread Bruce Fischl
   On Sat, Oct 19, 2019 at 12:16 PM Bruce Fischl wrote: Hi Vinny why do you need to brain structures from MNI space? Isn't the aseg sufficient? Or are there structures that are not in the aseg? cheers Bruce On Sat, 19 Oct 2019, Vinny K wrote

Re: [Freesurfer] FreeSurfer transforms

2019-10-19 Thread Bruce Fischl
Hi Vinny why do you need to brain structures from MNI space? Isn't the aseg sufficient? Or are there structures that are not in the aseg? cheers Bruce On Sat, 19 Oct 2019, Vinny K wrote: External Email - Use Caution Hi, FreeSurfer does a great job in registering atlas

Re: [Freesurfer] help

2019-10-19 Thread Bruce Fischl
Hi Asim can you give us a bit more information? Where does the brainmask come from? I believe we should detect the fact that the brainmask.mgz is different than the automatically created one (brainmask.auto.mgz) and use it instead. Note that the recon editing mode in freeview sets erased

Re: [Freesurfer] FreeSurfer mal list - please remove me

2019-10-17 Thread Bruce Fischl
or pretty much any mailing list email - they should all come with an "unsubscribe" link On Thu, 17 Oct 2019, Damion V Demeter wrote: External Email - Use Caution https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer Check the bottom of the page you used to sign up. :)

Re: [Freesurfer] R: R: R: R: recon-all skull stripping

2019-10-16 Thread Bruce Fischl
Da: freesurfer-boun...@nmr.mgh.harvard.edu per conto di Bruce Fischl Inviato: mercoledì 16 ottobre 2019 17:58 A: Freesurfer support list Oggetto: Re: [Freesurfer] R: R: R: recon-all skull stripping   Hi Marianna I think you can just run recon-all -s -skullstrip

Re: [Freesurfer] R: R: R: recon-all skull stripping

2019-10-16 Thread Bruce Fischl
the question is: does recon-all add optional flagged arguments to this function while running recon-all? and which of them? Thank you. BW Marianna Da: freesurfer-boun...@nmr.mgh.harvard.edu per conto di Bruce Fischl Inviato

Re: [Freesurfer] R: R: recon-all skull stripping

2019-10-16 Thread Bruce Fischl
...@nmr.mgh.harvard.edu On Behalf Of Bruce Fischl Sent: Wednesday, October 16, 2019 12:48 PM To: Freesurfer support list Subject: Re: [Freesurfer] R: R: recon-all skull stripping oh, sure, you can just run that part of recon-all. You don't need to rerun the whole thing cheers Bruce On Wed, 16 Oct

Re: [Freesurfer] R: R: recon-all skull stripping

2019-10-16 Thread Bruce Fischl
Da: freesurfer-boun...@nmr.mgh.harvard.edu per conto di Bruce Fischl Inviato: mercoledì 16 ottobre 2019 17:40 A: Freesurfer support list Oggetto: Re: [Freesurfer] R: recon-all skull stripping   Hi Marianna I'm not sure what you mean

Re: [Freesurfer] R: recon-all skull stripping

2019-10-16 Thread Bruce Fischl
W Marianna Da: freesurfer-boun...@nmr.mgh.harvard.edu per conto di Bruce Fischl Inviato: mercoledì 16 ottobre 2019 17:23 A: Freesurfer support list Oggetto: Re: [Freesurfer] recon-all skull stripping   Hi Marianna the skull stripping is a hybrid procedure that uses both a watershed

Re: [Freesurfer] recon-all skull stripping

2019-10-16 Thread Bruce Fischl
Hi Marianna the skull stripping is a hybrid procedure that uses both a watershed algorithm and a deformable surface. There is no single intensity threshold in it. Maybe I'm misunderstanding your question? There are parameters you can change (for example the preflooding height), but there is

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

2019-10-16 Thread Bruce Fischl
Hi Xiaoqian it's pretty hard to tell what's going on from these images. If you tar/gzip your whole subject dir and upload it with an email telling us the specific voxel coords that you want us to examine cheers Bruce On Wed, 16 Oct 2019, Xiaoqian Yan wrote: External Email - Use

Re: [Freesurfer] help

2019-10-14 Thread Bruce Fischl
Hi Asim if you edited the brainmask in recon-mode in freeview the edits will be detected and retained. cheers Bruce On Mon, 14 Oct 2019, Asim Hassan wrote: External Email - Use Caution Good afternoon, I would like to know is there a way to run recon-all on subjects in

Re: [Freesurfer] Mri_mask producing only zeros

2019-10-14 Thread Bruce Fischl
Hi Sara we will need to know the actual commands and the screen output from them that you ran cheers Bruce On Mon, 14 Oct 2019, Sims, Sara A (Campus) wrote: External Email - Use Caution Freesurfers, I am trying to use mri_mask using surface overlays. I made a label into

Re: [Freesurfer] mri_convert no scaling

2019-10-09 Thread Bruce Fischl
Hi Ezequiel -noscale 1 works in most cases, but here the analyze file itself specifies a scalling that is done as part of the reading process. If you want to disable it try (in tcsh): setenv FS_ANALYZE_NO_RESCALE 1 then run mri_convert as before. You should see an addition printout in the

Re: [Freesurfer] How to measure the cortical thickness in tumor patients?

2019-10-09 Thread Bruce Fischl
Hi James I think the -lh/-rh flags are for processing single (ex vivo) hemis, not for only processing one hemi in a whole-brain image. If you want to erase the hemi with the tumor it will probably work cheers Bruce On Wed, 9 Oct 2019, 王子谦 wrote: External Email - Use Caution  

Re: [Freesurfer] Brodmann area parcellation

2019-10-07 Thread Bruce Fischl
meaning you have to give recon-all the -all switch so it can create things like the lh.white surface cheers Bruce On Mon, 7 Oct 2019, Greve, Douglas N.,Ph.D. wrote: You can to run the full recon-all on a given subject's data, and it will create the broadmann areas On 10/5/2019 1:31 AM,

Re: [Freesurfer] Freesurfer - issue after installation in Linux

2019-10-03 Thread Bruce Fischl
yes, depending on your hardware it can take >12 hours, particularly if you aren't using -openmp On Thu, 3 Oct 2019, Theotonio Pauliquevis wrote: External Email - Use Caution Hi,  Thanks for the prompt reply.  After I installed tcsh it did run successfully.  Since this

Re: [Freesurfer] Freesurfer's last version installation

2019-10-03 Thread Bruce Fischl
Hi Vale I think it should happen by default, but definitely test it on one subject before you launch them all! Bruce On Thu, 3 Oct 2019, Barletta, Valeria wrote: > Dear Freesurfers, > We need to install the last version of Freesurfer, but we need to keep the > wm edits that we made with

Re: [Freesurfer] Curvature estimation from Hessian

2019-10-03 Thread Bruce Fischl
Hi Philipp the Hessian is estimated at each vertex by doing a quadratic fit to the local surface as the height function over the tangent plane of all the vertices in a 2-neighborhood of that vertex. I'm not sure what the gradient vanishing is about, but the curvatures are just the eigenvalues

Re: [Freesurfer] Exporting ROI segmentation in T1 DICOM header

2019-10-03 Thread Bruce Fischl
Hi Vânia you can convert the aparc+aseg.mgz to nifti and find something that goes from there to dicom, but we don't at the moment support writing dicom, although I think Paul (ccd) has worked on it and might have something to add cheers Bruce On Thu, 3 Oct 2019, Correia de Aguiar, V.M.

Re: [Freesurfer] Converting .label coordinates to MNI

2019-09-27 Thread Bruce Fischl
Hi Joel I believe they are stored in "tkreg ras" by default. In any case, mri_label2label should let you map them to pretty much any space you like. cheers Bruce On Fri, 27 Sep 2019, Berger, Joel wrote: External Email - Use Caution Hi friendly Freesurfers, I have seen

Re: [Freesurfer] Which files do I need to mri_deface to anonymized a subject?

2019-09-27 Thread Bruce Fischl
Hi Tim you probably also want to do the files in the orig dir (like orig/001.mgz). cheers Bruce On Fri, 27 Sep 2019, Tim Schäfer wrote: External Email - Use Caution Dear FS experts, I want to upload neuroimaging data pre-processed by FreeSurfer's recon-all pipeline to a consortium

Re: [Freesurfer] Error during processing data. mris_make_surfaces malloc: *** error for object 0x2431900024317: pointer being freed was not allocated.

2019-09-27 Thread Bruce Fischl
ok, we'll see if we can replicate it. On Fri, 27 Sep 2019, Троицкий Антон Александрович wrote: External Email - Use Caution Dear Bruce, I don't’ know exactly what happened during the processing.  I have 8 Gb of RAM of my Mac. When the freesurfer is working there is

Re: [Freesurfer] Error during processing. mris_make_surfaces(10174, 0x7fffbf9553c0) malloc: *** error for object 0x2431900024317: pointer being freed was not allocated/

2019-09-27 Thread Bruce Fischl
Hi, if you upload this entire subject to our ftp site we will take a look cheers Bruce On Fri, 27 Sep 2019, Троицкий Антон Александрович wrote: External Email - Use Caution Hello FreeSurfer Developers, during the processing of patient data an error occurred. I don’t

Re: [Freesurfer] Error during processing data. mris_make_surfaces malloc: *** error for object 0x2431900024317: pointer being freed was not allocated.

2019-09-24 Thread Bruce Fischl
Are you running out of memory on the machine? If not, and you upload the entire subject dir we will see if we can replicate and fix this problem. cheers Bruce On Tue, 24 Sep 2019, Троицкий Антон Александрович wrote: External Email - Use Caution Hello FreeSurfer Developers, during

Re: [Freesurfer] Keep manual edits of older freesurfer versions?

2019-09-23 Thread Bruce Fischl
in subsequent steps (measures extraction for group analyses, etc.)? Best, Joëlle __ De : freesurfer-boun...@nmr.mgh.harvard.edu de la part de Bruce Fischl Envoyé : lundi, 23 septembre 2019 20:04:46 À : Freesurfer support

Re: [Freesurfer] Keep manual edits of older freesurfer versions?

2019-09-23 Thread Bruce Fischl
Hi Joëlle why not cp the whole 5.1 dir to a 6.0 dir, then run recon-all in the 6.0 dir (so all the directories are prepopulated with the 5.1 edits so they can be preserved) cheers Bruce On Mon, 23 Sep 2019, Joëlle Ismay Rosanne Van Der Molen wrote: External Email - Use Caution  

Re: [Freesurfer] talairach.m3z not found

2019-09-23 Thread Bruce Fischl
Hi Vasudev that means recon-all didn't complete. Try rerunning with -make all cheers Bruce On Mon, 23 Sep 2019, Dev vasu wrote: External Email - Use Caution Dear all, When i run recon-all , i am encountering an error transforms/ talairach.m3z not found during registration

Re: [Freesurfer] Fwd: Talairach Failure Dection error for recon-all

2019-09-23 Thread Bruce Fischl
Hi Hang have you looked at the talairach transform? If it is accurate you can just tell recon-all to ignore it. If it is not, maybe you can run the SPM bias correction later in the stream? cheers Bruce On Mon, 23 Sep 2019, Hang Zeng wrote: External Email - Use Caution

Re: [Freesurfer] FS6.0 on 2yo subjects

2019-09-18 Thread Bruce Fischl
Hi Dimitrios it's kind of an empirical question. Lilla does have some newer tools you might consider instead of things aren't as accurate as you want cheers Bruce On Wed, 18 Sep 2019, Alexopoulos, Dimitrios wrote: External Email - Use Caution We have acquired 0.8mm

Re: [Freesurfer] How to fasten recon-all execution time without using CUDA

2019-09-18 Thread Bruce Fischl
Hi Vasudev -openmp N is the best way at the moment. Do you actually have 3 cores to dedicate? Usually due to memory access speeds and such we don't see much gain after N=4, but I'm surprised there is no effect cheers Bruce On Wed, 18 Sep 2019, Dev vasu wrote: External Email - Use

Re: [Freesurfer] mris_sphere question

2019-09-17 Thread Bruce Fischl
it starts a few steps before mris_spheres, so I have to redo and often crashes again. Thank you for your help! Best, Michael -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Bruce Fischl Sent: Tuesday, September 17, 2019 10:16 AM To: Freesurfer support list S

Re: [Freesurfer] mris_sphere question

2019-09-17 Thread Bruce Fischl
Hi Michael I think that is the last message that mris_sphere prints so I believe it has finished. Does it exit with an error message or just keep running forever? Bruce On Tue, 17 Sep 2019, Lauricella, Michael wrote: External Email - Use Caution Dear Freesurfer Experts,

Re: [Freesurfer] Downsampling from fsaverage to fsaverage6

2019-09-13 Thread Bruce Fischl
has not only binary values (0 or 1) it is made of float values, whereas the output mri_surf2surf contains only binary values. Best, Matthieu On 13/09/2019 15:52, Bruce Fischl wrote: Hi Matthieu sorry, I don't understand. All the files are binary, no? Are you getting an error

Re: [Freesurfer] Downsampling from fsaverage to fsaverage6

2019-09-13 Thread Bruce Fischl
Hi Matthieu sorry, I don't understand. All the files are binary, no? Are you getting an error? cheers Bruce On Fri, 13 Sep 2019, Matthieu VANHOUTTE wrote: External Email - Use Caution Dear FS's experts, I am trying to downsample some surface data from fsaverage to fsaverage6 with

Re: [Freesurfer] Hippocampal-subfields-T1 interruption (Bruce Fischl)

2019-09-13 Thread Bruce Fischl
,freesurfer-requ...@nmr.mgh.harvard.edu 写道: Re: Hippocampal-subfields-T1 interruption (Bruce Fischl) ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer

Re: [Freesurfer] Hippocampal-subfields-T1 interruption

2019-09-12 Thread Bruce Fischl
Hi Guodong Hmmm, not sure what is doing that, but my guess is you have mv aliased. Can you type: which mv and see if you have it aliased to "mv -i" or some such? cheers Bruce On Thu, 12 Sep 2019, 3 6 wrote: External Email - Use Caution Hello FreeSurfer Developers, I'm

Re: [Freesurfer] Additional scans in hippocampal subfields segmentation

2019-09-11 Thread Bruce Fischl
, at 15:53, Bruce Fischl wrote: Hi Antonin can you give us the details of your T2-FLAIR? Certainly it helps us generate more accurate pial surfaces by avoiding dura. For the subfields I defer to Eugenio cheers Bruce On Thu, 5 Sep 2019, Rovai Antonin wrote: External Email - Use Caution

Re: [Freesurfer] Morphological Features, Description & References

2019-09-09 Thread Bruce Fischl
. Winkler's   srf2vol matlab script. On 9/6/2019 10:22 AM, Bruce Fischl wrote: Hi Philipp I'll leave the volume question to Doug. The curvatures are estimated by fitting a second order polynomial to the local height function in the tangent bundle then computing the Hessian using the white (gray

Re: [Freesurfer] error while running "-hippocampal-subfields-T1" with Freesurfer 6.0

2019-09-09 Thread Bruce Fischl
Hi Shahrazd can you try: chmod -R a+rx $FREESURFER_HOME/bin and see if that fixes your problem? Bruce On Mon, 9 Sep 2019, shahrzad kharabian wrote: External Email - Use Caution Hi,  I have already run recon-all with default options on a large set of T1-weighted images,

Re: [Freesurfer] Correcting defect problem after checking skull stripped and editing wm.mgz

2019-09-09 Thread Bruce Fischl
Hi Jiun-Wei have you looked at the ?h.defect_labels overlaid on the inflated.nofix and orig.nofix surfaces? That will tell you where the defect is that is causing you trouble. If you have lesions they may be the source of the issue. If you can't sort it out you can tar and gzip the entire

Re: [Freesurfer] multiple T2s

2019-09-08 Thread Bruce Fischl
Hi Aaron you may need to motion correct and average them yourself. We'll put it on our feature request list though cheers Bruce On Sat, 7 Sep 2019, Aaron Tanenbaum wrote: External Email - Use Caution Does freesurfer 6.0 have the ability to use multiple T2s in recon-all. If

Re: [Freesurfer] Interruption during data processing

2019-09-06 Thread Bruce Fischl
Hi Anton recon-all -sd -s -make all should do the trick cheers Bruce On Fri, 6 Sep 2019, Троицкий Антон Александрович wrote: External Email - Use Caution Bruce, could you explain how can I do that? I mean what command should I use and parameters? Best regards, Anton Troitskii

Re: [Freesurfer] Morphological Features, Description & References

2019-09-06 Thread Bruce Fischl
Hi Philipp I'll leave the volume question to Doug. The curvatures are estimated by fitting a second order polynomial to the local height function in the tangent bundle then computing the Hessian using the white (gray/white boundary) surface. We also have some discrete measures of curvature

Re: [Freesurfer] Using mask image

2019-09-05 Thread Bruce Fischl
Hi Gwang-Won try mri_mask cheers Bruce On Fri, 6 Sep 2019, Gwang-Won Kim wrote: External Email - Use Caution Hi there,   I would like to show activation map in the thalamus, caudate nucleus, and hippocampus.   activation.mgh : activation map in the subcortical areas

Re: [Freesurfer] How to generate a solid volume from lh/rh.pial-outer-smoothed

2019-09-05 Thread Bruce Fischl
Hi Miao try using mris_fill instead. I think it defaults to 0.5mm resolution, but this can be changed with -r cheers Bruce On Thu, 5 Sep 2019, Jingya Miao wrote: External Email - Use Caution Hello Freesurfer Developers, I am trying to generate a solid volume out of the

Re: [Freesurfer] Interruption during data processing

2019-09-05 Thread Bruce Fischl
you should be able to use the -make all target in recon-all to only rerun the steps that are required cheers Bruce On Thu, 5 Sep 2019, Троицкий Антон Александрович wrote: External Email - Use Caution Dear freesurfer users, I encountered a problem when data processing suddenly

Re: [Freesurfer] Additional scans in hippocampal subfields segmentation

2019-09-05 Thread Bruce Fischl
Hi Antonin can you give us the details of your T2-FLAIR? Certainly it helps us generate more accurate pial surfaces by avoiding dura. For the subfields I defer to Eugenio cheers Bruce On Thu, 5 Sep 2019, Rovai Antonin wrote: External Email - Use Caution I’m resending this request

Re: [Freesurfer] recon_all cuda 9.1

2019-09-04 Thread Bruce Fischl
Hi Vasudev what does "very slowly" mean? cheers Bruce On Wed, 4 Sep 2019, Dev vasu wrote: External Email - Use Caution Dear, I tried running recon-all -s subjectname -t subjectid -all -openmp 15 , and it still runs very slowly. Is there a faster way to reduce the recon-all

Re: [Freesurfer] FreeView : Tools : Volume Filter : Close

2019-09-04 Thread Bruce Fischl
Hi Yar, close is a morphological close operation, which in the grayscale case is a max followed by a min I believe (in a 3x3x3 nbhd) cheers Bruce On Wed, 4 Sep 2019, Yasir Hadi wrote: External Email - Use Caution Hello FreeSurfer Developers, I just want to get the

Re: [Freesurfer] -conform option in mri_convert produces crazy artefacts

2019-09-04 Thread Bruce Fischl
www.erasme.ulb.ac.be Disclaimer : http://www.erasme.ulb.ac.be/email-disclaimer On 3 Sep 2019, at 16:57, Bruce Fischl wrote: hmmm. Can you tar and gzip the whole subject dir and upload it to our ftp site? On Tue, 3 Sep 2019, Rovai Antonin wrote: External Email - Use Caution Hey So opening

Re: [Freesurfer] -conform option in mri_convert produces crazy artefacts

2019-09-03 Thread Bruce Fischl
, Bruce Fischl wrote: Hi Antonin hmmm. Can you try *only* loading the conformed image and seeing how it looks? freeview will use one of the images as the basis for it's display coordinates, which can cause apparent slicing artifacts that are only display issues for other volumes. cheers Bruce

Re: [Freesurfer] -conform option in mri_convert produces crazy artefacts

2019-09-03 Thread Bruce Fischl
Hi Antonin hmmm. Can you try *only* loading the conformed image and seeing how it looks? freeview will use one of the images as the basis for it's display coordinates, which can cause apparent slicing artifacts that are only display issues for other volumes. cheers Bruce On Tue, 3 Sep

Re: [Freesurfer] Reconall with no-MPRAGE T1w image?

2019-09-03 Thread Bruce Fischl
MRI) and it also has an inversion pulse (also CNR isn’t as good as in a MPRAGE). Best Antonin On 3 Sep 2019, at 15:44, Bruce Fischl wrote: Hi AR 1. mprage in general has higher CNR and lower SNR than non inversion-prepared T1w sequences like FLASH. THe -mprage switch takes

Re: [Freesurfer] Reconall with no-MPRAGE T1w image?

2019-09-03 Thread Bruce Fischl
Hi AR 1. mprage in general has higher CNR and lower SNR than non inversion-prepared T1w sequences like FLASH. THe -mprage switch takes advantage of this to loosen the intensity gradient threshold in the region filling of the wm. 2. If you just leave out the -mprage switch it will revert to

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

2019-08-30 Thread Bruce Fischl
oh, the export command is failing? You mentioned you weren't running bash (which is the shell that knows what to do with an export command). Can you install bash? If not, you can use setenv instead of export and the .csh file instead of the .sh On Fri, 30 Aug 2019, michele rizzi wrote:  

Re: [Freesurfer] Substancia-Nigra ROI

2019-08-30 Thread Bruce Fischl
sorry, Substancia Nigra is also on our list of next structures to be released, but it is not ready yet cheers Bruce On Sat, 31 Aug 2019, Gwang-Won Kim wrote: External Email - Use Caution Hi there,   I would like to make a ROI for a left Substanci Nigra. It is possible

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

2019-08-30 Thread Bruce Fischl
Hi Mike can you send us the full command line and screen output? And are you running bash? What operating system? thanks Bruce On Fri, 30 Aug 2019, michele rizzi wrote: External Email - Use Caution Dear All during freesurfer installation, I type export

Re: [Freesurfer] I have a question for subthalamic nucleus ROI.

2019-08-30 Thread Bruce Fischl
Hi Gwang-Won sorry, the STN is high on our to-do list, but we don't have anything distributable yet. cheers Bruce On Fri, 30 Aug 2019, Gwang-Won Kim wrote: External Email - Use Caution   Hi there,   I would like to make a ROI for subthalamic nucleus. But, there is not

Re: [Freesurfer] how to get the displacement from template to the linearly registered image

2019-08-29 Thread Bruce Fischl
Hi Ping we don't apply the linear registration to any image - we use it to initialize the nonlinear warp. And yes, the nonlinear warp is stored as a 128^3 array with 2 voxel spacing and interpolation between them. You can visualize the .m3z directly in freeview as a 3-frame displacement

Re: [Freesurfer] how to get the displacement from template to the linearly registered image

2019-08-28 Thread Bruce Fischl
Hi Ping the displacement fields are stored in m3z format in the file talairach.m3z. They are a vector field over the atlas that maps points in the atlas to points in the original (not linearly aligned) space. cheers Bruce On Wed, 28 Aug 2019, ping cao wrote: External Email -

Re: [Freesurfer] binary version of brainmask?

2019-08-26 Thread Bruce Fischl
oxels in the brain are considered to be non-brain? > > From: freesurfer-boun...@nmr.mgh.harvard.edu > On Behalf Of Bruce Fischl > Sent: Tuesday, 27 August 2019 12:18 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] binary version of brainmask? > > Hi Chris &g

Re: [Freesurfer] binary version of brainmask?

2019-08-26 Thread Bruce Fischl
Hi Chris can't you just use mri_binarize to turn whichever want you want into a binary mask? Or mri_threshold for that matter cheers Bruce On Tue, 27 Aug 2019, Chris Adamson wrote: External Email - Use Caution Freesurfer,   Is it possible to get mri_watershed to produce

Re: [Freesurfer] recon_all hires

2019-08-23 Thread Bruce Fischl
Hi Mona if you upload your gzipped and tarred subject dir we will take a look (or if it is somewhere accessible just point us to the network location and give us access) cheers Bruce On Fri, 23 Aug 2019, falk.luesebr...@med.ovgu.de wrote: External Email - Use Caution

Re: [Freesurfer] what is the right manual correction when ?h.white extends into gray matter

2019-08-22 Thread Bruce Fischl
Hi Carolin yes, there are ways. You can modify the intensity thresholds that mris_make_surfaces auto-detects. Sounds like they are a bit off. If you send us the recon-all.log and the intensity of a few voxels that are included in the ?h.white surface and should not be we can suggest some

Re: [Freesurfer] mris_convert segmentation fault on R hemisphere aparc.a2009s only?

2019-08-22 Thread Bruce Fischl
  On Thu, Aug 22, 2019 at 1:39 PM Bruce Fischl wrote: Hi Damion you can upload them to our ftp site https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange cheers Bruce On Sun, 18 Aug 2019, Damion V Demeter wrote

Re: [Freesurfer] mris_convert segmentation fault on R hemisphere aparc.a2009s only?

2019-08-22 Thread Bruce Fischl
Hi Damion you can upload them to our ftp site https://surfer.nmr.mgh.harvard.edu/fswiki/FtpFileExchange cheers Bruce On Sun, 18 Aug 2019, Damion V Demeter wrote: External Email - Use Caution Hi Bruce,  My apologizes, I just saw this reply because I didn't realize I

Re: [Freesurfer] apart.a2009s naming convention: from "_and_" to "&"

2019-08-17 Thread Bruce Fischl
for the fold in the atlas stats file (which would list 0 vertices and NaNs for the mean thickness and other measurements), but the whole entry is missing instead. That's fine, you just have to be aware of it. Tim On August 16, 2019 at 4:02 PM Bruce Fischl wrote: Hi Tim I think

Re: [Freesurfer] apart.a2009s naming convention: from "_and_" to "&"

2019-08-16 Thread Bruce Fischl
Hi Tim I think that is the nature of the parcellation - there are some small folds that don't occur in all subjects. cheers Bruce On Thu, 15 Aug 2019, Tim Schäfer wrote: External Email - Use Caution Another interesting thing I noticed, which may be of interest to anybody parsing

Re: [Freesurfer] mris_convert segmentation fault on R hemisphere aparc.a2009s only?

2019-08-15 Thread Bruce Fischl
Hi Damion if you upload the relevant files so that we can replicate this we will fix it cheers Bruce On Wed, 14 Aug 2019, Damion V Demeter wrote: External Email - Use Caution I am having an issue processing some of my subjects through the HCP pipeline and have no idea what

Re: [Freesurfer] overlay on subcortical surfaces

2019-08-12 Thread Bruce Fischl
Hi Catarina I'm not sure how you would do a surface overlay for a volumetric structure. Where would you map the interior of it? cheers Bruce On Mon, 12 Aug 2019, cr...@cam.ac.uk wrote: External Email - Use Caution Dear Freesurfer Experts, As it happens for cortical

Re: [Freesurfer] CORRECTING DEFECT

2019-08-09 Thread Bruce Fischl
Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent: Friday, August 9, 2019 11:00 AM To: Freesurfer support list Subject: Re: [Freesurfer] CORRECTING DEFECT CAUTION: External they are an overlay not a surface. Load

Re: [Freesurfer] CORRECTING DEFECT

2019-08-09 Thread Bruce Fischl
imported lh.defect_labels as an overlay over the lh.inflated.nofix but the values aren't 1-30 they're 0 - 160 roughly. I'm not sure why... Thanks! -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl Sent

Re: [Freesurfer] CORRECTING DEFECT

2019-08-09 Thread Bruce Fischl
Of Bruce Fischl Sent: Friday, August 9, 2019 10:27 AM To: Freesurfer support list Subject: Re: [Freesurfer] CORRECTING DEFECT CAUTION: External Hi Brendan the time to correct goes with the square of the size of the defect (actually the convex hull of the defect) so it can take a very long time

Re: [Freesurfer] CORRECTING DEFECT

2019-08-09 Thread Bruce Fischl
Hi Brendan the time to correct goes with the square of the size of the defect (actually the convex hull of the defect) so it can take a very long time for big ones. More importantly, if the defect is that large it may not be corrected in the anatomically desired manner. You should take a look

Re: [Freesurfer] Fwd: Recon-all output space and .annot file registration

2019-08-07 Thread Bruce Fischl
Hi Rachel all processing is done in the subject's native space. If you want to downsample probably the easiest thing to do is map to one of the lower res fsaverage subjects (e.g. fsaverage3 or fsaverage4) using mri_surf2surf/mri_label2label and the like after running recon-all. cheers Bruce

Re: [Freesurfer] [External] Re: mri_deface fails on pediatric brain

2019-08-05 Thread Bruce Fischl
urrently using Centos7 as the base image to build our freesurfer container, > but we can run it on any other Linux based OSes. As far as our hardware goes, > we run on variety of hardware including HPC system, public and private cloud > platforms and a few dedicated desktop machines at our lab

Re: [Freesurfer] FreeSurfer Import File

2019-08-05 Thread Bruce Fischl
you will need to extract them from the archive into a directory, then give recon-all a *single* dicom file from each T1-weighted series that you want to motion correct and average (if you only hae one, then just specify one). Something like: recon-all -i -sd \ -s -all cheers Bruce On

Re: [Freesurfer] A Question Regarding Topology Correction

2019-08-05 Thread Bruce Fischl
Hi Maedeh there are a bunch of steps involved in the topology correction that you will need to run (e.g. surface inflation, quasi-homeomorphic spherical mapping, etc...). If you can synthesize a T1-ish image you can just run it through recon-all and it should do the right thing. Otherwise you

Re: [Freesurfer] [External] Re: mri_deface fails on pediatric brain

2019-08-04 Thread Bruce Fischl
to surfer.nmr.mgh.harvard.edu ftp server (named t1.nii.gz).Thank you for looking into this problem. Soichi On Sun, Aug 4, 2019 at 10:35 AM Bruce Fischl wrote: This message was sent from a non-IU address. Please exercise caution when clicking links or opening attachments from external

Re: [Freesurfer] mri_deface fails on pediatric brain

2019-08-04 Thread Bruce Fischl
Hi Soichi mri_deface isn't really supported anymore, but if you upload a subject that fails I'll take a look. I would have thought in the ABCD subject age range it would work cheers Bruce On Sat, 3 Aug 2019, Soichi Hayashi wrote: External Email - Use Caution Hello. We

Re: [Freesurfer] recon-all exited with ERRORS

2019-08-03 Thread Bruce Fischl
hmmm, what system are you running on in terms of software and hardware? I don't see any errors in the log file so I'm not sure why it stopped. You should be able to rerun these subjects with -make all to complete them cheers Bruce On Sat, 3 Aug 2019, Kuo Li wrote: External Email -

Re: [Freesurfer] Failure of mri_robust_template in fmriprep

2019-07-31 Thread Bruce Fischl
sure, but them on our ftp site and we'll see if we can replicate it. I'll also cc Martin so he can comment cheers Bruce On Wed, 31 Jul 2019, Frederick, Blaise B. wrote: Ø  Hi Blaise Ø    * I can't even find an exit(-9) in the code. If you can track down and send us the inputs to

Re: [Freesurfer] WM surface including too much gray matter

2019-07-29 Thread Bruce Fischl
om: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Monday, July 29, 2019 9:29 AM > To: Freesurfer support list > Subject: Re: [Freesurfer] WM surface including too much gray matter

Re: [Freesurfer] WM surface including too much gray matter

2019-07-29 Thread Bruce Fischl
Hi Brian usually this is fixable by changing some default parameters in recon-all. You can try this yourself (the intensity bounds used in mri_segment and mris_make_surfaces - look at the help), or you can upload a subject to our ftp site and we can recommend some cheers Bruce On

Re: [Freesurfer] Error running recon-all

2019-07-25 Thread Bruce Fischl
Hi Vin are you sure you have space on that disk? Can you run: mri_info /home/Downloads/reorient/test.nii mri_info /media/results/mri/orig/001.mgz ls -l /media/results/mri/orig/001.mgz /media/results/mri/rawavg.mgz and send us the results? cheers Bruce On Thu, 25 Jul 2019, vin rasa wrote:

Re: [Freesurfer] T1 orientation prior to running recon-all

2019-07-24 Thread Bruce Fischl
Hi Abid nope, you shouldn't have to, as long as the header info is correct. Does it come up properly in freeview? That is, does what freeview thinks the orientations are match what they really are? cheers Bruce On Wed, 24 Jul 2019, Abid Qureshi wrote: External Email - Use

Re: [Freesurfer] Multiple overlays onto surface

2019-07-24 Thread Bruce Fischl
Hi Zeynab tksurfer has been deprecated for years. Can you use freeview instead? You can do this in freeview by loading one as a "curvature" map and the other as an overlay cheers Bruce On Wed, 24 Jul 2019, Alshelh, Zeynab wrote: Hi Freesurfers, Is it possible to view two overlays on

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