Re: [Freesurfer] How to create my own ASEG and APARC atlases

erage here? -input flash5_avg.mgz \ # Should I set the T2W-SPACE average here? Cheers, Arsene 2018-06-04 21:32 GMT+02:00 Bruce Fischl : Hi Arselle the node_spacing is the mm resolution of the atlas Markov priors and class-conditional densities, the prior_spacing i

Re: [Freesurfer] How to create my own ASEG and APARC atlases

Hi Arselle the node_spacing is the mm resolution of the atlas Markov priors and class-conditional densities, the prior_spacing is the same for the classwise spatial priors the equivalent for the surface is mris_ca_train. It takes annot files as input cheers Bruce On Mon, 4 Jun 2018,

Re: [Freesurfer] Unpacking Philips scans work-around... should this work?

Hi Stephanie you shouldn't have to create the directory structure or anything. If you have nifti files you can give those to recon-all as input in the same way you would dicom (with -i directories and do it's thing cheers Bruce On Sat, 2 Jun 2018, DeCross, Stephanie N. wrote: Hi, I have

Re: [Freesurfer] Cortical thickness and cortical stroke

on behalf of Bruce Fischl Sent: Thursday, May 31, 2018 1:09 PM To: Freesurfer support list Subject: Re: [Freesurfer] Cortical thickness and cortical stroke   Hi Guillaume I certainly wouldn't trust the thickness values anywhere near the lesion. What exactly are you trying to compute? cheers

Re: [Freesurfer] creating a mask for the thalamus parcellations

not yet, sorry. We are working on it Bruce On Thu, 31 May 2018, Erik O'Hanlon wrote: >External Email - Use Caution > > Dear FS Experts, > > > Is it possible to use the labels found in the FreesurferColourLUT.txt for the > Thalamus parcellations (8001-8014) using the

Re: [Freesurfer] white matter and grey matter

r + grey matter of brain. How can i get > this ? > > Also, I looked at aparc+aseg.mgz, when i try to see 3D of it, using > free-view. I see half brain in 3D. How can i see the 3D of segmented brain. > > Thanks, > Ritesh Mahajan > > - Original Message - > From:

Re: [Freesurfer] Cortical thickness and cortical stroke

Hi Guillaume I certainly wouldn't trust the thickness values anywhere near the lesion. What exactly are you trying to compute? cheers Bruce On Thu, 31 May 2018, Guillaume Bellanger wrote: External Email - Use Caution Hi Freesurfers users, I am looking on cortical

Re: [Freesurfer] midbrain mask in standard-space?

] midbrain mask in standard-space?       External Email - Use Caution    The "brainstem pipeline" described here: https: //surfer.nmr.mgh.harvard.edu/fswiki/BrainstemSubstructures Thanks! -Dan On Wed, 30 May 2018, Bruce Fischl wrote: > Hi Dan > > which brainste

Re: [Freesurfer] midbrain mask in standard-space?

Hi Dan which brainstem atlas do you mean? cheers Bruce On Wed, 30 May 2018, djpet...@u.washington.edu wrote: >External Email - Use Caution > > Hi Freesurfer email list, > > I'm trying to get the midbrain mask from the brainstem segmentation > pipeline into standard space, for use

Re: [Freesurfer] manual edits

? Thanks ​Sent with ProtonMail Secure Email.​ ‐‐‐ Original Message ‐‐‐ On May 30, 2018 11:27 AM, Bruce Fischl wrote: Hi John I'm not sure I understand exactly what you are referring to. We automatically fill in the ventricles so that they are contained within the interior

Re: [Freesurfer] manual edits

Hi John I'm not sure I understand exactly what you are referring to. We automatically fill in the ventricles so that they are contained within the interior of the ?h.white surfaces. Is that what you thought was incorrect? cheers Bruce On Wed, 30 May 2018, John Anderson wrote:

Re: [Freesurfer] white matter and grey matter

Hi Ritesh can you clarify what you mean? Do you want a segmentation? You can get that in the aparc+aseg.mgz at the end of the recon-all processing. cheers Bruce On Wed, 30 May 2018, Ritesh Mahajan wrote: >External Email - Use Caution > > Hello Team, > > 1) How can i just get the white

Re: [Freesurfer] mri_label2label: Empty label file

Hi Emmanuel you need to send us the complete command line and screen output of the commands that failed if we are going to help you cheers Bruce On Tue, 29 May 2018, Emmanuel Nwosu wrote: External Email - Use Caution Dear FreeSurfer users, I want to extract the

Re: [Freesurfer] RAS coordinates for inflated surface

patience and support! Giulia 2018-05-25 15:52 GMT+02:00 Bruce Fischl <fis...@nmr.mgh.harvard.edu>: Hi Giulia, no, that shouldn't be the case. You don't care about the RAS coordinates of the inflated vertex - only its index. Use the index to look up the corresponding

Re: [Freesurfer] RAS coordinates for inflated surface

works with surface electrodes, not depth electrodes. Best wishes, Giulia  On Thu, 24 May 2018 at 23:22, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: Hi Giulia find the vertex index of the vertex you are interested in, then read the surface whose RAS coordinates yo

Re: [Freesurfer] RAS coordinates for inflated surface

Hi Giulia find the vertex index of the vertex you are interested in, then read the surface whose RAS coordinates you want (e.g. the white or pial) and lookup the RAS coords of the vertex at that index. cheers Bruce On Thu, 24 May 2018, Giulia Liberati wrote: External Email - Use

Re: [Freesurfer] fthresh function in tksurfer

Hi Srishti tksurfer has been deprecated for a pretty long time now. Can you try freeview instead? cheers Bruce On Tue, 22 May 2018, srishti goel wrote: External Email - Use Caution Hello, I am trying to view network based maps produced from a meta-analysis using neuroelf

Re: [Freesurfer] Displaying insular electrode contacts on an inflated brain surface

Hi Giulia once you have the vertex index on any surface (e.g. the lh.white) you can lookup that vertex on any other surface in the same hemi (e.g. lh.inflated). Probably the easiest thing to do is create a label file and sample it to the white surface. Then it will show properly on the

Re: [Freesurfer] voxels with mislabeled hemisphere

Hi Catarina that is indeed strange. Can you upload one subject (the entire dir) and tell us the voxel coords of one of these points so we can take a look? cheers Bruce On Fri, 18 May 2018, Catarina Saiote wrote: External Email - Use Caution Hi freesurfer team, I found

Re: [Freesurfer] Definition of anatomical features

Hi S.V they are all volumes I think. The definitions can be found in various Kennedy/Caviness papers (which we cite in our original 2002 aseg paper in Neuron). cheers Bruce On Fri, 18 May 2018, SJ JV wrote: External Email - Use Caution Hi Can someone please give the

Re: [Freesurfer] gcs and gca to coordinates

Hi Tim the gcs files are on the surface, so it is not so trivial.If you are looking for MNI coords probably the easiest thing to do is use the .annot files that we distribute with fsaverage. For the .gca, you can convert a "frame" of it to a nifti volume via: mri_convert file.gca#0

Re: [Freesurfer] macOS Sierra installation error

Hi Narae Try running bash first Cheers Bruce > On May 14, 2018, at 10:57 PM, NR K wrote: > > Narae ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mailman/listinfo/freesurfer The

Re: [Freesurfer] correcting surface with optic chiam

Hi Jim it probably doesn't matter, except for aesthetics cheers Bruce On Fri, 11 May 2018, Alexopoulos, Dimitrios wrote: External Email - Use Caution In many of our studies there appears to be a pial/wm surface associated with the optic chiasm. (See attached). Do these

Re: [Freesurfer] how to reinsert volume geometry information into surf

Hi Padma I think if you use mris_convert -vol-geom it will copy the voluem geometry from the mri volume you specify cheers Bruce On Fri, 11 May 2018, padma wrote: Hi, I exported a freesurfer mesh to PLY format to do some computation and have exported the PLY surface back to an fsmesh.

Re: [Freesurfer] run recon all with forced orientation, spacing and dimension

t; > Please can you explain why this happening ? > > Thanks, > Ritesh Mahajan > > - Original Message - > From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> > To: "freesurfer" <freesurfer@nmr.mgh.harvard.edu> > Sent: Thursday, May 10, 20

Re: [Freesurfer] run recon all with forced orientation, spacing and dimension

) ? > > Thanks, > Ritesh Mahajan > > - Original Message - > From: "Bruce Fischl" <fis...@nmr.mgh.harvard.edu> > To: "freesurfer" <freesurfer@nmr.mgh.harvard.edu> > Sent: Thursday, May 10, 2018 8:22:38 PM > Subject: Re: [Freesurfer] run

Re: [Freesurfer] run recon all with forced orientation, spacing and dimension

Hi Ritesh your best bet is to run everything normally, then convert the output to whatever format/orientation/voxel size you want cheers Bruce On Thu, 10 May 2018, Ritesh Mahajan wrote: >External Email - Use Caution > > Thank you Bruse. Actually i converted the input into RAI

Re: [Freesurfer] run recon all with forced orientation, spacing and dimension

Hi Ritesh no, not really. What is your goal? We should handle any input orientation as long as it is specified in the headers. cheers Bruce On Thu, 10 May 2018, Ritesh Mahajan wrote: >External Email - Use Caution > > Hello Team, > > As i know free-surfer generates the output with

Re: [Freesurfer] Fw: Query regarding creation of atlas directly from probabilistic information

9131-8522898 *From:* Mageshwar Selvakumar <mageshwar.selvaku...@outlook.com> *Sent:* Monday, April 23, 2018 10:36 AM *To:* freesurfer@nmr.mgh.harvard.edu; Bruce Fischl *Subject:* Query regarding creation of atlas directly from probabilistic information

Re: [Freesurfer] Problems at exporting recon-all outputs

Hi Miguel I think in Christophe's atlas not all folds occur in all subjects. cheers Bruce On Sat, 5 May 2018, Miguel Ángel Rivas Fernández wrote: External Email - Use Caution Hi Freesurfer developers, After having executed the recon-all in several subjects I tried to

Re: [Freesurfer] mri_segment-MRIcheckVolDims error

Hi Kambiz we need more information than this to help you. Can you send us the full recon-all command you ran and the recon-all.log? cheers Bruce On Thu, 3 May 2018, Kambiz Tavabi wrote: External Email - Use Caution Hi all, I noticed the following error message in a

Re: [Freesurfer] Starting with Neuroimaging

Hi Lan we have tutorials on our wiki with associated data that you could try going through cheers Bruce On Wed, 2 May 2018, Lan Naoyuki wrote: External Email - Use Caution Hello Freesurfer experts, I am a junior in Computer Science, and am planning to join a neuroimaging

Re: [Freesurfer] problem using mri_vol2label for subcortical regions

May 2018, at 16:01, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: Hi Lucia can you cc the list so others can answer? You can't get a surface-based label for a subcortical region as they aren't on (or close) to the surrface. I think mri_vol2label is the right binary to create a volumetr

Re: [Freesurfer] Problems Extending the Pial Surface

that are computed automatically in mris_make_surfaces. You can see them if you look in your recon-all.log. For example if the lowest value gm is allowed to be at the pial surface is too high, then it will settle too far in  Thanks, Cheers,   2018-04-29 17:33 GMT+02:00 Bruce Fischl <

Re: [Freesurfer] problem using mri_vol2label for subcortical regions

Hi Lucia 8 is cerebellar cortex - how could you sample it to the neocortical surface? I'm not sure I understand what you are trying to do. Bruce On Mon, 30 Apr 2018, Lucia Billeci wrote: External Email - Use Caution Dear Freesurfer Experts, I want to use mri_vol2label to

Re: [Freesurfer] orig.mgz versus T1.mgz

Hi Colleen it depends on what you want to do. The T1.mgz probably isn't the correct volume to use in any case. The orig.mgz is close to the raw data (e.g. it has a skull in it and has not been bias corrected). If you want a skull-stripped, bias-corrected version you could use either the

Re: [Freesurfer] Problems Extending the Pial Surface

surface. To solve this error could I use the control points? When I use the control points, will I also be able to correct the white matter segmentation? I send you a image if you want to check it. Thank you very much! Cheers, [IMAGE]   2018-04-27 21:28 GMT+02:00 Bruce Fischl <

Re: [Freesurfer] cannot find subject

Hi Heidi can you give us the full screen output and exact command you are running? And what shell are you using? In csh/tcsh you can have an env variable be superseded with a set command. For example: setenv SUBJECTS_DIR right set SUBJECTS_DIR=wrong will cause getenv to get wrong. Also, try

Re: [Freesurfer] mri_ca_register

Hi Aaron that is for longitudinal analysis. We have been trying to document this kind of thing, but there are still gaps cheers Bruce On Fri, 27 Apr 2018, Aaron Tanenbaum wrote: External Email - Use Caution Hello FreeSurfers, I am trying to find what the -l flag does

Re: [Freesurfer] Problems Extending the Pial Surface

Hi Saum it is, but you need to figure out why it isn't getting out far enough. The easiest way is to override the intensity statistics that are computed automatically in mris_make_surfaces. You can see them if you look in your recon-all.log. For example if the lowest value gm is allowed to be

Re: [Freesurfer] vertex wise cortical thickness within ROIs

vertex-wise volume using -th3. What option should I use to get a list of absolute cortical thickness for each vertex within ROI? Thank you again, Hisako -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Bruce Fischl

Re: [Freesurfer] vertex wise cortical thickness within ROIs

Hi Hisako you can use mris_anatomical_stats for this purpose. cheers Bruce On Fri, 27 Apr 2018, Fujiwara, Hisako wrote: External Email - Use Caution Hello FreeSurfer Developers,   I'm attempting to compute absolute cortical thickness for each vertices within anatomical

Re: [Freesurfer] mri_watershed error/global region of the brain empty

I think so. Or apply it with mri_convert -at On Fri, 27 Apr 2018, miracle ozzoude wrote: External Email - Use Caution Hello Bruce,  Thanks. Can I use tkregisterfv to visualize it? Best,  Paul On Fri, Apr 27, 2018 at 11:37 AM, Bruce Fischl <fis...@nmr.mgh.harvard.

Re: [Freesurfer] mri_watershed error/global region of the brain empty

Hi Paul that usually means something went wrong before the watershed. Check the input image to make sure that it and the talairach_with_skull.lta are ok cheers Bruce On Fri, 27 Apr 2018, miracle ozzoude wrote: External Email - Use Caution Hello FreeSurfer,  While

Re: [Freesurfer] ?h.area

Hi Joost I think you can do it with mris_make_surfaces by setting the number of iterations to 0 (-n 0) so it doesn't do any deformation, and starting with the surface you want to end with (e.g. -orig_white white) cheers Bruce On Fri, 27 Apr 2018, Joost Janssen wrote: External

Re: [Freesurfer] Using mprage flag.

if you have an mprage it usually helps a bit cheers Bruce On Thu, 26 Apr 2018, Aaron Tanenbaum wrote: External Email - Use Caution Hello FreeSurfers When should I use the MPRAGE flag for recon-all?  Aaron Tanenbaum ___

Re: [Freesurfer] mri_compute_volume_fractions

ror reading inplaneres from 002_S/mri/aseg.mgz >> regio_read_register(): Success >> Error reading inplaneres from 002_S/mri/aseg.mgz >> mri_compute_volume_fractions: could not load registration file from >> 002_S/mri/aseg.mgz >> >> >> Thanks, >> Dhivya

Re: [Freesurfer] mri_compute_volume_fractions

__ > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > Sent: Wednesday, April 25, 2018 6:21 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] mri_compute_volume_fra

Re: [Freesurfer] recon-all with T1 and T2 images

Hi Heidi it is easy to imagine there being a regionally specific bias between processing so you are better off doing them all the same way cheers Bruce On Wed, 25 Apr 2018, Heidi Lindroth wrote: External Email - Use Caution Hello,  I have processed the majority of my T1

Re: [Freesurfer] mri_compute_volume_fractions

tions: could not load registration file from > mri/aseg.mgz > > Thanks, > Dhivya > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce Fischl > [fis...@nmr.mgh.harvard.edu] > S

Re: [Freesurfer] mri_compute_volume_fractions

n this format which the documentation says, > > mri_compute_volume_fractions [options] --o --reg > > Am I going wrong somewhere? > > Thanks, > Dhivya > > From: freesurfer-boun...@nmr.mgh.harvard.edu > [freesurfer-boun...@nmr.mgh.harva

Re: [Freesurfer] mri_compute_volume_fractions

Hi Dhivya if you are doing it in the space of the anatomicals, then use identity.nofile as the reg file (which is a special file name that will internally create an identity matrix). The output stem is whatever you pick - it will be prepended to the files that are written with the volume

Re: [Freesurfer] Segmentation issue with FS6

Hi Cody yes, it could be due to poor contrast. The watershed isn't the issue though, it is mri_segment and mris_make_surfaces. You can try changing the wm/gm limits, or upload the subject and we will take a look cheers Bruce On Tue, 24 Apr 2018, Barlow, Cody wrote: External Email

Re: [Freesurfer] correcting deffect

that's a pretty large defect - about 15% of the size of a typical surface. The defect correction complexity is quadratic in the convex hull of the defect, so it can take a *long* time for big defects. Usually one this big means something went badly wrong - a bunch of skull attached, or

Re: [Freesurfer] Lateral Geniculate Nucleus (LGN) roi or volume measures?

Hi Yash we hae some prototypes for LGN but nothing ready for primetime yet sorry Bruce On Mon, 16 Apr 2018, Yash Patel wrote: Hi all,  Is there any way to obtain (automatically, n~1000 subjects), LGN volumes from the Freesurfer set of tools?  Or somehow transform the ROI from an atlas into

Re: [Freesurfer] problem with mri_label2vol for aseg

Hi Michelle from the mri dir I think you can run: mri_convert -rl rawavg.mgz -rt nearest aseg.mgz aseg.rawavg.mgz -rl = "reslice like" -rt = "resample type" cheers Bruce p.s. I think your problem is probably that you used trilinear resampling. YOu could change the resampling in mri_vol2vol

Re: [Freesurfer] Segmentation of anterior and posterior commissures

Hi Antonin unfortunately the atlas subjects were not collected with an IRB that allows us to distribute them. We are working to update the atlas with data we can distribute, but that is not a short-term solution. You second proposal would work I imagine cheers Bruce On Sat, 14 Apr 2018,

Re: [Freesurfer] Visualizing Single anatomical ROI on FreeView

you can use mri_extract_label on the aseg.mgz to pull out just the label you want, then load it and the MRI into freeview (if that is what you mean) cheers Bruce On Fri, 13 Apr 2018, Srinivasan, Dhivya wrote: > Hi, > > I am attempting to view single anatomical ROI (say Right-Hippocampus) >

Re: [Freesurfer] tksurkfer save error

yes,, there is a command line option (-ss I think) cheers Bruce On Thu, 12 Apr 2018, Douglas N. Greve wrote: We are not really supporting tksurfer anymore. You can use freeview to save a png from the GUI. Ruopeng, is there a way to take a snap shot from the command line? On 04/12/2018

Re: [Freesurfer] tksurkfer save error

Hi Jen tksurfer is deprecated and this sounds like an error in your graphics environment. Have you tried using freeview instead? Generating snapshots should be pretty easy cheers Bruce On Thu, 12 Apr 2018, Evans, Jennifer (NIH/NIMH) [F] wrote:     Hi,   This is a repost as I didn’t

Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

p.s. you probably want to grab a new freeview also, as it lets you jump to the voxel coords of each control point so you can see them On Wed, 11 Apr 2018, Hoopes, Andrew wrote: Hi Anna,   You can download the new mri_normalize from this link -

Re: [Freesurfer] mri_vol2surf: unable to compare volume maps

g Research and Life Experiences Lab > University of North Carolina at Chapel Hill > email (W): srish...@email.unc.edu > skype: srishti.goel12 > > >> On Sun, Apr 8, 2018 at 11:00 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> >> wrote: >> Hi Srishti >>

Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

b > University of North Carolina at Chapel Hill > email (W): srish...@email.unc.edu > skype: srishti.goel12 > > > On Thu, Apr 5, 2018 at 12:43 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: >       let's see if it works.

Re: [Freesurfer] mri_vol2surf: unable to compare volume maps

Hi Srishti the directory you are in doesn't matter. YOu either need to set SUBJECTS_DIR in the environment, or use --sd to specify the directory that contains your subjects. I think you can also give it the full path to a target volume if you want, but maybe Doug can comment as he knows this

Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

/Clinical Research Specialist Child Imaging Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srish...@email.unc.edu skype: srishti.goel12 On Thu, Apr 5, 2018 at 12:43 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: let's see if it

Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

Research and Life Experiences Lab University of North Carolina at Chapel Hill email (W): srish...@email.unc.edu skype: srishti.goel12 On Thu, Apr 5, 2018 at 12:31 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: Hi Srishti if you look in the subject's scripts dir there

Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

@email.unc.edu skype: srishti.goel12 On Thu, Apr 5, 2018 at 12:24 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: if you run the command that failed again on the command line directly (that is, not in recon-all) does it fail again? On Thu, 5 Apr 2018, srishti goel wr

Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

Experiences Lab University of North Carolina at Chapel Hill email (W): srish...@email.unc.edu skype: srishti.goel12 On Thu, Apr 5, 2018 at 12:16 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: Hi Srishti are you sure that your machine didn't just run out of memory? The

Re: [Freesurfer] recon-all: exited with errors (white matter peak at 110, cannot allocate memory)

Hi Srishti are you sure that your machine didn't just run out of memory? The recon-all.log file includes the amount of free (and total) memory at the time the process was started. cheers Bruce On Thu, 5 Apr 2018, srishti goel wrote: Hi, I have been trying to edit structural brains and

Re: [Freesurfer] query regarding creating an atlas from nifti volumes.

Universität Erlangen Nürnberg Office: Fahrstr. 17, 91054 Erlangen Phone: + 49-9131-8522898 From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of

Re: [Freesurfer] query regarding creating an atlas from nifti volumes.

Hi Mageshwar what kind of an atlas are you talking about? We have multiple atlases for different purposes. cheers Bruce On Thu, 5 Apr 2018, Mageshwar Selvakumar wrote: Dear All, I am a newbie to freesurfer and I would like to use our in-house built probabilistic atlas(each region as a

Re: [Freesurfer] error rerunning recon-all (exited with ERRORS)

Hi Anna from your log file it looks like some other process is using more than 2/3 of the memory on your machine: total used free sharedbuffers cached Mem: 24729588 1685252478770644095060 0 10543292 -/+ buffers/cache:6309232

Re: [Freesurfer] Unsubscribing

Hi Barnali every FreeSurfer list message comes with a link to a list management page at the bottom (as most well-maintained list messages do). You can take yourself off whenever you want. cheers Bruce On Wed, 4 Apr 2018, Barnali Basu wrote: Hi , I have not used this for years, could you

Re: [Freesurfer] extracting morphometric values from co-ordinates

Hi Emmanuel, you could create a label in MNI coords, then map it to a group of subjects using mri_label2label. "Value at a point" only makes sense for point measures like thickness though. cheers Bruce On Wed, 4 Apr 2018, Emmanuel Nwosu wrote: > Dear FreeSurfer Experts, > > Am wondering

Re: [Freesurfer] using T2 for hippo subfields

no it is not required cheers Bruce On Wed, 4 Apr 2018, Alexopoulos, Dimitrios wrote: Per an earlier post below, is an 'expert_file' always required when using the -hires option? Jim From:

[Freesurfer] Fwd: Learning Workshop in Bloomington IN (fwd)

FYI -- Forwarded message -- Date: Tue, 3 Apr 2018 11:14:38 -0400 From: Satrajit Ghosh <sa...@mit.edu> To: Bruce Fischl <fis...@nmr.mgh.harvard.edu>, "Jog, Amod" <a...@mgh.harvard.edu> Subject: Fwd: Learning Workshop in Bloomington IN hi,  thi

Re: [Freesurfer] mri_watershed Error: indices out of bounds

Can you send us the recon-all.log? > On Mar 30, 2018, at 11:32 AM, Darko Komnenić wrote: > > Dear experts, > while running recon-all on FreeSurfer 5.1.0 I encountered the following error: > mri_watershed Error: indices out of bounds > > I searched the email archive and

Re: [Freesurfer] defining input images in a for-loop in recon-all

-all command. From: Bruce Fischl <fis...@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] defining input images in a for-loop in recon-all To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Message-ID: <alpine.lrh.2.20.1803291007011.1...@gate.nmr.mgh.harva

Re: [Freesurfer] defining input images in a for-loop in recon-all

Hi Darko sorry, you need to sort this out yourself as there is no way for us to know where the dicoms are. An alternative is to create each subject dir, create the 00?.mgz files (if you have more than one acquistion) in the /mri/orig dir, then run recon-all without the -i flag. If you use -i

Re: [Freesurfer] tkmedit: no tools window

Hi Gina tkmedit has been deprecated for many years. Can you try using freeview instead? cheers Bruce On Tue, 27 Mar 2018, gj wrote: > Hi, > > When I launch tkmedit, I only get the "Display" window with no "Tools" > window so I don't have any menus (I wanted to overlay a label file -- > not

Re: [Freesurfer] Tessellation of hippocampus

when you say it was not working, what did you try? And are you trying to cover the surface of the entire hippocampus? We need the command line and full screen output of whatever you ran, and a more detailed description of what you are trying to accomplish cheers Bruce On Mon, 26 Mar 2018,

Re: [Freesurfer] Volume are different in asegstats vs matlab

Hi Kristine the aseg.stats volume uses partial volume correction to get subvoxel accuracy. cheers Bruce On Fri, 23 Mar 2018, Lee Subin Kristine wrote: Hi,   I have a question about volume info from freesurfer vs matlab. I am looking at, say, the left hippocampus volume from asegstats,

Re: [Freesurfer] Skull stripping error - too much brain lost - solved

ies. The log file indicates "surface validation has detected possible Error" Does this suggest a more meaningful defect in the base image or something that can be corrected via other parameters or manual editing? Log file attached. Thanks, -Matt Bruce Fischl Fri, 02 Mar 2018 08:00:11 -

Re: [Freesurfer] Correnting image bias before segmentation and parcelation - due to frontal and occipital shading.

, Mar 18, 2018 at 3:19 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: Hi Gabriel you can try adding control points in the white matter in those regions, but typically when there is so much signal loss there is very little anatomical SNR left to build

Re: [Freesurfer] mri_segment error

-all.log file in attach thanks a lot On Fri, Feb 9, 2018 at 2:22 PM, Z Hessam <z.hes...@gmail.com> wrote: thank you for your attention regards On Fri, Feb 9, 2018 at 1:04 AM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: looks like the acquisition is not what you would

Re: [Freesurfer] Cortical volume parcellation

Hi Mark the easiest thing to do would be to draw the label you want on the fsaverage surface, then use mri_label2label to map from there to each of your individual subjects cheers Bruce On Sun, 18 Mar 2018, Mark Wagshul wrote: > Hi. I'm new to using Freesurfer. We are using the parc + aseg

Re: [Freesurfer] Correnting image bias before segmentation and parcelation - due to frontal and occipital shading.

Hi Gabriel you can try adding control points in the white matter in those regions, but typically when there is so much signal loss there is very little anatomical SNR left to build models with. good luck Bruce On Sun, 18 Mar 2018, Gamaliz wrote: [IMAGE] On Sun, Mar 18, 2018 at 2:28 AM,

Re: [Freesurfer] (no subject)

Hi Sudeshna according to our local neuranatomical expert: it is probably ventral claustrum (ventral claustrum stretches in to the temporal lobe ,especially at the anteriorly (slightly anterior to amygdala). so this region is not cortex and you shouldn't worry about the surfaces there.

Re: [Freesurfer] Get center coordinates of ROIs from the Lausanne2008 parcellation

Hi Laura, the .gcs file is a probabilistic atlas with lots of information such as neighborhood clique potentials. You are probably better off applying it to fsaverage and computing the centroids of parcels in that space. cheers Bruce On Wed, 14 Mar 2018, Laura Juan Galmes wrote: Hi

Re: [Freesurfer] Freesurfer6.0 failure

Hi Naka we have tracked down this problem and should have a patch soon cheers Bruce On Tue, 13 Mar 2018, Naka Beguedou wrote: > > > Hello, > I allow myself to send you this mail in order to have some informations. we > have a problem concerning the segmentation of FREESURFER6.0 > Indeed for

Re: [Freesurfer] Negative areas in mris_sphere, dark in freeview

oun...@nmr.mgh.harvard.edu> On Behalf Of Bruce Fischl Sent: Tuesday, 13 March 2018 12:44 PM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer] Negative areas in mris_sphere, dark in freeview hmmm, then maybe it is something else? If you email me a surface I'll s

Re: [Freesurfer] Negative areas in mris_sphere, dark in freeview

, Chris Adamson wrote: I had already done this, it had no effect. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Bruce Fischl Sent: Tuesday, 13 March 2018 12:39 AM To: Freesurfer support list <f

Re: [Freesurfer] Negative areas in mris_sphere, dark in freeview

dices, no effect. Chris. -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> On Behalf Of Bruce Fischl Sent: Saturday, 10 March 2018 1:06 AM To: Freesurfer support list <freesurfer@nmr.mgh.harvard.edu> Subject: Re: [Freesurfer]

Re: [Freesurfer] mri_ca_normalize error: Abort (core dumped)

Hi Theresa can you open the inputs to mri_ca_normalize in freeview ok? The nu.mgz for example? Please send us the recon-all.log so we can examine it. If all the inputs look fine, then upload your subject and we will have a look. cheers Bruce On Fri, 9 Mar 2018, Marschall, T.M. wrote:

Re: [Freesurfer] RECON-ALL {Disarmed}

Hi Zheng can you please include the full command you ran, the full screen output and the recon-all.log file? cheers Bruce On Fri, 9 Mar 2018, 郑凤莲 wrote: Hi experts, I am using FS 6.0 to calculate LGI. But when l ran recon-all, there is an error: couldn't find DWI parameters. I don't

Re: [Freesurfer] Negative areas in mris_sphere, dark in freeview

Hi Chris this probably means that the triangles aren't constructed according to our conventions. The ordering in faces is important as the cross-product of the legs of each triangle have to point outwards. That's how we define the surface normal vector field. Sounds like whatever software you

Re: [Freesurfer] Mean Curvature

ail. Sent with ProtonMail Secure Email.​ ‐‐‐ Original Message ‐‐‐ On March 8, 2018 4:13 PM, Bruce Fischl <fis...@nmr.mgh.harvard.edu> wrote: Hi Kaspar I don't think so. cheers Bruce On Thu, 8 Mar 2018, Kasper Jessen wrote: Hej FreeSurfer, Question regarding the meancurv extracted

Re: [Freesurfer] Brainstem registration

Hi Chungmin do you have a whole-brain T1 that you can use for generating anatomical models? If so, many more things are possible cheers Bruce On Thu, 8 Mar 2018, Chungmin Han wrote: Dear whomever it may concern, I'm Chungmin, a graduate research assistant in University of Texas at

Re: [Freesurfer] Question regarding recon-all

? From: freesurfer-boun...@nmr.mgh.harvard.edu <freesurfer-boun...@nmr.mgh.harvard.edu> on behalf of Bruce Fischl <fis...@nmr.mgh.harvard.edu> Sent: Thursday, March 8, 2018 1:37 PM To: Freesurfer support list Subject: Re: [Freesurfer] Question regarding recon-all Hi Dan yes, we typi

Re: [Freesurfer] Question regarding recon-all

Hi Dan yes, we typically use -i and read in the dicoms directly, but you can do it for a nifti also. Or you could create the 001.mgz and not use it, but there is no reason to (it's just more work). cheers Bruce On Thu, 8 Mar 2018, Levitas, Daniel wrote: Hello, I am running recon-all

<    5   6   7   8   9   10   11   12   13   14   >