Re: [Freesurfer] WM surface on pial surface and pial surface out of brain

Hi Bruno it looks to me like there is very little gray/white contrast, which is the root of your problem. YOu could try limiting the intensity ranges in the segmentation and surface deformation steps using expert options (e.g. -wlo for mri_segment). We can also help improve the acquisition. If

Re: [Freesurfer] Skull stripping quality assessment

Hi Adam the most common metric would involve doing a manual stripping, usually of a T2. Note that in FS we designed it using a risk-minimization approach that weighs removing brain as much more costly (~10x I think) then leaving around skull. cheers Bruce On Mon, 17 Feb 2020, Adam Rytina wr

Re: [Freesurfer] watershed, saving issue

Hi Kirill I think this is a question for Matti (now ccd) cheers Bruce On Fri, 14 Feb 2020, Kirill Elin wrote: External Email - Use Caution Hallo everybody, I am not entirely sure whether this is FreeSurfer error actually. I am doing first recon all which completes without e

Re: [Freesurfer] Recon-all autorecon2 exited with error

Hi Ben you need to rerun autorecon3 also otherwise some of the results will be new and some old and the surfaces/overlays (like thickness) will be inconsistent cheers Bruce On Wed, 12 Feb 2020, Benjamin Ineichen wrote: External Email - Use Caution Dear Freesurfer experts,

Re: [Freesurfer] Affine registration 2 input images

Hi Adam yes, mri_robust_register should do the trick. You will need to specify --affine as rigid is the default cheers Bruce On Fri, 7 Feb 2020, Adam Rytina wrote: External Email - Use Caution Hello all, I need to perform an affine registration between two input images. P

Re: [Freesurfer] mri_deface error: could not find wm peak

Hi Tim if you upload the input files to mri_deface and the full command line I'll take a look. Is this the dev version you are using? cheers Bruce On Mon, 3 Feb 2020, Tim Schäfer wrote: External Email - Use Caution Dear FreeSurfer experts, I am running mri_deface for all relevant

Re: [Freesurfer] Pial surface not including parts of cortex

Hi Monica sure, if you tar and gzip the entire subject dir and ftp it to us, then send us a description that includes the voxel coords of where you think things should be more accurate we will take a look cheers Bruce On Fri, 31 Jan 2020, Monica Bondy wrote: External Email - Use

Re: [Freesurfer] recon-all errors - mri_segstats and mri_relabel_hypointensities

From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl Sent: Tuesday, January 28, 2020 3:37 PM To: Freesurfer support list Cc: Greve, Douglas N.,Ph.D. Subject: Re: [Freesurfer] recon-all errors - mri_segstats and mri_relabel_hypointensities

Re: [Freesurfer] XL defect in recon-all

Hi Devika these types of huge defects usually mean something dramatic has gone wrong with e.g. the skull stripping. Even if it completes it is unlikely to generate accurate surfaces. Check the ?h.inflated.nofix and ?h.orig.nofix over the wm.mgz and you will likely find the issue quicky cheers

Re: [Freesurfer] Tuning WM threshold

Hi Paul yes, the -mprage flag could definitely cause what you are seeing. It assume higher CNR and lower SNR in the images (hence bigger class separation between gray and white), and if used on SPGR it could definitely erode boundaries like this. cheers Bruce On Fri, 31 Jan 2020, Wright, Pau

Re: [Freesurfer] Error Bad CPU

Hi Philipp does this happen for all the FS executables? What kind of machine are you trying it from and who installed it? Sounds like you are on a mac and maybe trying to use a version installed for a different kind of computer cheers Bruce On Thu, 30 Jan 2020, Philipp Barzyk wrote:

Re: [Freesurfer] Xl defect in Freesurfer

Hi Devika the very large defects can take a very long time to fix, and probably won't produce good results. They are typically caused by something significant going wrong - large portions of the skull left behind and connected to the surface, an incorrect aseg, that kind of thing. You should

Re: [Freesurfer] recon-all errors - mri_segstats and mri_relabel_hypointensities

Hi Laurel if a subject dir already exists recon-all will exit unless you specify -force. Alternatively you can try using the -make all flag, which should rerun only the steps that are needed (assuming the reboot didn't happen e.g. in the middle of writing a file) cheers Bruce On Tue, 28 Jan

Re: [Freesurfer] Desikan and Destrieux Atlas information

Hi Louise 1. All the spatial, distributional and markov info we detailed in our methods paper (priors at each point, markov priors in principal directions and means and variances of geometry, all stored per label 2. It is on the surface/sphere. 3. Not trivially, but the code is open source

Re: [Freesurfer] Change the subject ID after recon-all?

, so this is very helpful. All the best, Tim -- Dr. Tim Schäfer Postdoc Computational Neuroimaging Department of Child and Adolescent Psychiatry, Psychosomatics and Psychotherapy University Hospital Frankfurt, Goethe University Frankfurt am Main, Germany On January 21, 2020 at 11:02 PM Bruce

Re: [Freesurfer] Change the subject ID after recon-all?

Hi Antonin and Tim you should be able to do: setenv FS_SKIP_TAGS 1 mri_convert vol_with_tags.mgz vol_without_tags.mgz and verify it worked with mri_info cheers Bruce On Tue, 21 Jan 2020, Antonin Skoch wrote: External Email - Use Caution Hi, Tim, the subject ID can be also c

Re: [Freesurfer] question about curv.mgh

Hi Rafael the ?h.curv files are spatially smoothed mean curvature cheers Bruce On Tue, 21 Jan 2020, Raffaele Dubbioso wrote: External Email - Use Caution Hello FS team,  can you please tell me what is the measurement scale of the curv.mg file? Is it a mean curvature (mm-1)

Re: [Freesurfer] Freesurfer Digest, Vol 191, Issue 29

   2. registration of dwi images (Sam W)    3. Re: registration of dwi images (Yendiki, Anastasia)    4. Project hippocampus to inflated 3D model? (Mohammad Rashid)    5. Re: aparcstats2table error (Devika K)    6. Re: Project hippocampus to inflated 3D model? (Bruce

Re: [Freesurfer] aparcstats2table error

Hi Devika In the future can you include the text of the command and the output in your email instead of a screenshot? That will make our job easier. Try specifying which subjects you want processed explicitly with --subjects cheers Bruce On Sun, 19 Jan 2020, Devika K wrote: Ex

Re: [Freesurfer] Project hippocampus to inflated 3D model?

Hi Mohammad you can use mri_tessellate or mri_mc to build a mesh model of the hippocampus from the aseg if you want, then use mris_inflate on it. You will lose internal structure though. cheers Bruce On Sun, 19 Jan 2020, Mohammad Rashid wrote: External Email - Use Caution

Re: [Freesurfer] Results in different size

Hi Marina how did you create your average inflated surface? mris_inflate typically normalizes the scale of the inflated surface to have the same total surface area as the input surface (so for the less-folded inflated surface it has to become bigger). I guess you could try running it directly

Re: [Freesurfer] Calculate thickness in a ROI volume

Hi Karel you can specify a label to mris_anatomical_stats with the -l option cheers Bruce On Fri, 17 Jan 2020, Karel Mauricio Lopez Vilaret wrote: External Email - Use Caution Dear Freesurfer team, I would like to get the thickness values of a specific ROI (volume mask).

Re: [Freesurfer] Oval shape in average subject inflated

Hi Marina for the lower res fsaverage subjects you probably want to decrease the number of iterations of the inflation. For fsaverage6 you could try: mris_inflate -n 5 lh.smoothwm lh.inflated.new it should be just a min or two so you can try different values for the -n switch cheers Bruce

Re: [Freesurfer] Right Lateral Ventricle Omitted from white and pial surfaces

if the gray matter you are interested looks ok then you should be fine Bruce On Tue, 14 Jan 2020, Rachel Hoel wrote: External Email - Use Caution Thank you, I am still checking in with my supervisors about sending the subject. For now, if we are only interested in looking at

Re: [Freesurfer] Skipping bias field correction

set of bias corrected images (probably using ANTs). The plan is to extract regional and whole brain volumes for these T1-weighted images. Regards Patrick On Tuesday, January 14, 2020, 6:45:20 AM GMT+5:30, Bruce Fischl wrote: I agree with Matt. We do multiple stages of bias correection to

Re: [Freesurfer] Skipping bias field correction

I agree with Matt. We do multiple stages of bias correection to flatten things out as much as possible. Can you give us an idea of what you are trying to achieve? On Mon, 13 Jan 2020, Glasser, Matthew wrote: External Email - Use Caution Why do you want to do that?  FreeSurfe

Re: [Freesurfer] Anterior parts of Temporal Lobe missing

Hi Meike can you send us some images? And what volume are the intensity values around 73 for white matter? That is way to low for the norm.mgz or the brain*.mgz cheers Bruce On Fri, 10 Jan 2020, Meike Hettwer wrote: >External Email - Use Caution > > Hi everyone, > > I am currently work

Re: [Freesurfer] Fixing wm/gm in brain with a cyst

Hi Laurel yes, I think that is the way to go, but it's hard to tell for sure only looking at one slice. cheers Bruce On Thu, 9 Jan 2020, Laurel Quinlan wrote: External Email - Use Caution Hi FS Support, I am working on manual edits to a brain with a suspected cyst. Attache

Re: [Freesurfer] Projection on fsaverage5

Hi Marina how do you project to fsaverage5? cheers Bruce On Wed, 8 Jan 2020, Marina Fernández wrote: External Email - Use Caution Dear Freesurfer experts, I would like to convert the individual preprocessed EPI volume (that it is normalized to MNI152 space and without smoothin

Re: [Freesurfer] Question regarding T1 map from spoiled 3D GRE

Hi Joe do you know what the forward model for VIBE is? mri_ms_fitparms uses the FLASH forward model of image formation then does a max likelihood estimation of the T1/T2*/PD using that model. If VIBE is a different model then it certainly won't work. cheers Bruce On Sun, 5 Jan 2020, joe va

Re: [Freesurfer] Inflation cortical hemisphere to sphere in Freesurfer !?

no, and it isn't inflation, strictly speaking. The spherical mapping minimizes metric distortion, which to us is more neuroscientifically plausible. The conformal maps minimize (local) angular distortion and push all the distortion into area compression and expansion. Metric distortion minimize

Re: [Freesurfer] Getting issue in running bt_recon

Hi Sudhakar if you want us to help you we will need a lot more information. What exact command did you run? What was the entire screen output? What kind of computer are you running it on? That kind of thing cheers Bruce On Sat, 4 Jan 2020, sudhakar Mishra wrote: External Email -

Re: [Freesurfer] Run Recon-all Parallel on Linux

on-all -s {.} -i {} -all -qcache", after installing Xcode and Homebrew.) But I couldn't find any similar information on the Linux platform. Regards Frank On Jan 3, 2020 11:15 PM, Bruce Fischl wrote: Hi Frank do you mean completing a single recon faster? The easiest way to

Re: [Freesurfer] Run Recon-all Parallel on Linux

Hi Frank do you mean completing a single recon faster? The easiest way to do that is to use the -openmp flag, and set to the number of threads/cores you want to use. Alternatively if you have enough RAM you can just run multiple recon-alls at the same time (which will give you a bigger effe

Re: [Freesurfer] recon-all in freesurfer

no, sorry, it is not cheers Bruce On Thu, 2 Jan 2020, Fatemeh Ahmadi wrote: External Email - Use Caution Dear all, I'm working on brain surface with conformal geometry algorithms, I need to know whether triangular mesh that gets from "recon-all" in Freesurfer is a Delaunay tria

Re: [Freesurfer] Error in MATLAB while using freesurfer commands

using Winrar and renamed it subject-0001.mgh and this time it showed this >> error: >> ERROR: could not open C:\Users\home\Desktop\Project >> code\QuickNATv2\SampleDatasample-0001.mgh for reading >> ERROR: loading C:\Users\home\Desktop\Project >> code\QuickNATv2\Sampl

Re: [Freesurfer] Error in MATLAB while using freesurfer commands

Hi Mahdi can you run mri_info in a Linux shell on that file and send us the entire screen output? cheers Bruce On Sun, 29 Dec 2019, mahdi mahdavi wrote: External Email - Use Caution Hi. I'm a medical student and I'm trying to use the QuickNATv2 MATLAB code for structural MR

Re: [Freesurfer] intensity map

Hi Zhang 1. the aseg.stats should contains statistics on intensities in various structures. 2. Do you want a surface or a measurement at each point? If you want a surface use mris_expand, if just a measure use mri_vol2surf with a projfrac of 0.5 cheers Bruce On Sun, 29 Dec 2019, a Chines

Re: [Freesurfer] Lateral ventricles mask

Hi Tamir you can use mri_binarize --match or mri_extract_labels. cheers Bruce On Fri, 27 Dec 2019, Tamir Eisenstein wrote: External Email - Use Caution Dear FS experts, How can I create a binary mask of the lateral ventricles based on the ASEG output? Thanks! Tamir ___

Re: [Freesurfer] BA_exvivo.thresh.stats

Hi Sarah I'm not sure I understand. The smoothing doesn't really matter as the BAs reflect the location along the cortical sheet in spherical coordinates cheers Bruce On Sun, 29 Dec 2019, sarah.kloep...@web.de wrote: External Email - Use Caution Hi,     Do the Brodmann par

Re: [Freesurfer] Save output as attach file

gards Nader Neuroimaging phd student On 21 Dec 2019 18:36, "Bruce Fischl" wrote: sorry, can you clarify what you mean? Isn't the attachment already a saved output of freeview? I don't understand what you are trying to do cheers Bruce

Re: [Freesurfer] Save output as attach file

sorry, can you clarify what you mean? Isn't the attachment already a saved output of freeview? I don't understand what you are trying to do cheers Bruce On Sat, 21 Dec 2019, Nader Razmara wrote: External Email - Use Caution Dear I want to save output of freeview as attach f

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

Bruce, Thanks for the info. Can the tool display the vertexes with low G/W contrast? I would like to use those vertexes as a guide for visual evaluation. Cheers, Yawu Bruce Fischl 于 2019年12月19日周四 16:52写道： Hi Yawu we have tools for mapping G/W contrast and CNR, but of course that

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

Hi Yawu we have tools for mapping G/W contrast and CNR, but of course that presupposes that our surfaces are in the correct location (more or less). You can for example use vol2surf to sample at negative and positive proj_dist and compute this kind of thing, or I believe Doug has some binarie

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

Hi Cody not sure we have a binary for this, but it would be about 5 lines of matlab code cheers Bruce On Thu, 19 Dec 2019, cody samth wrote: External Email - Use Caution Hi, I was wondering if there is any automated command/method to create a new label that consists of the

Re: [Freesurfer] Conversion fMRI volumes to surface

Hi Marina yes, mri_vol2surf will sample volumes onto the surface. You will need to register them first (we typically use Doug Greve's bbregister for this). What preprocessing did you do? For cortical data we don't recommend smoothing in the volume - you are much better off sampling to the surf

Re: [Freesurfer] (no subject)

sorry, my fault. That was for someone else On Mon, 16 Dec 2019, Boris Rauchmann wrote: External Email - Use Caution This is the log when I´m creating this file: Boriss-MacBook-Pro:BN_Atlas_freesurfer boris$ mri_ca_label $SUBJECTS_DIR/1122/mri/brain.mgz $SUBJECTS_DIR/1122/mri

Re: [Freesurfer] (no subject)

to summarize, I want a warp that: foreach subject compute warp based on curvature apply warp to a functional overlay add that functional overlay to avg return (tf.reduce_mean(tf.square(avg))) make sense? So maximizing the mean squared average acivation On Mon, 16 Dec 2019, Boris Rau

Re: [Freesurfer] ROI analysis with manually created labels

Hi Yuanyuan this is really more of a batch processing/shell scripting question than a FreeSurfer one. Something like (in tcsh) set SUBJECTS = (N001 N002...) foreach s ($SUBJECTS) mris_anatomical_stats -l lh.precentral.label -t lh.thickness -b \ -f $s/stats/lh.precentra

Re: [Freesurfer] Cortical segmentation error

Hi Monica hmmm, hard to say without seeing the dataset. You could try using expert options to change some of the intensity thresholds if this is something specific to your acquiisition. If you upload the gzipped subject dir we will take a look cheers Bruce On Fri, 13 Dec 2019, Monica Bondy

Re: [Freesurfer] Create translucent brain volume and save as matlab figure file

Hi Sparsh probably easiest to do with a surface, but I defer to Ruopeng cheers Bruce On Fri, 13 Dec 2019, Sparsh Jain wrote: External Email - Use Caution Hi! Can I create a brain volume with about 40% opacity and save it as a matlab figure? The volume may not be very accur

Re: [Freesurfer] Segmentation fault mri_em_register

Hi Ricardo hmmm, the fact that it says "MRImaskDifferentGeometry" suggests that your skull stripping didn't end up "conforming", which is probably the error. Try something like: cp brainmask.mgz brainmask.bet.mgz mri_convert -rl orig.mgz brainmask.bet.mgz brainmask.mgz then rerun and see if

Re: [Freesurfer] Creating intermediate surfaces between white and pial?

Hi Tim mris_expand -thickness ... should do the trick. If you specify -thickness it will read in the ?h.thickness file and interpret the argument as a percentage of thickness, which is what you want I think cheers Bruce On Thu, 12 Dec 2019, Tim Schäfer wrote: External Email - Us

Re: [Freesurfer] (no subject)

Hi Boris can you send us the full command line and screen output of the commands that are failing? cheers Bruce On Thu, 12 Dec 2019, Boris Rauchmann wrote: External Email - Use Caution Thanks. unfortunately I get an error message when I use the --aseg flag for BN_Atlas_s

Re: [Freesurfer] Topological Defect

AM Bruce Fischl wrote: Does your 3D model need to be topologically correct? What are you trying to achieve? And are the holes/handles due to the tumor? Can you send us some images? cheers Bruce On Tue, 10 Dec 2019, Kong Chuizheng wrote

Re: [Freesurfer] Topological Defect

ill in the tumor do you mean adding the hollow part of the brain in wm.mgz? Best, Chuizheng Kong On Dec 10, 2019, at 12:07 PM, Bruce Fischl wrote: have you looked at our tutorial on topology fixing? I would try that first. You might need to fill in the tumor in the wm.mgz.

Re: [Freesurfer] Topological Defect

n Tue, Dec 10, 2019 at 8:58 AM Bruce Fischl wrote: Does your 3D model need to be topologically correct? What are you trying to achieve? And are the holes/handles due to the tumor? Can you send us some images? cheers Bruce On Tue, 10 Dec 2019, Kong Chuizheng

Re: [Freesurfer] Topological Defect

Does your 3D model need to be topologically correct? What are you trying to achieve? And are the holes/handles due to the tumor? Can you send us some images? cheers Bruce On Tue, 10 Dec 2019, Kong Chuizheng wrote: External Email - Use Caution Hello Freesurfer Developers,   

Re: [Freesurfer] Is subcortical segmentation reliable when cortical segmentation fails?

Hi Fredrik yes, the subcortical segmentation can still be ok when the cortical stream results are not that good cheers Bruce On Tue, 10 Dec 2019, Fredrik wrote: External Email - Use Caution Hi FreeSurfer experts,   In our data, we have a sample of older people with brain

Re: [Freesurfer] intensity map

Hi Zhang look at the docs for mri_vol2surf. In particular, check out the various --proj* options like projfrac and projdist cheers Bruce On Tue, 10 Dec 2019, a Chinese reader wrote: External Email - Use Caution Dear Freesurfer experts, I have some questions about intensit

Re: [Freesurfer] Recon-all

can you check to see if there is a large defect that is too big to fix? You should be able to see this in the log file or by checking the output of the job it is waiting for (PID 175414) On Tue, 10 Dec 2019, Gwang-Won Kim wrote: External Email - Use Caution Hi there,   I tr

Re: [Freesurfer] topological defect error

s gray/white matter that should be > included in the pial line? > > Thanks! > > -Laurel > > >___ _ > From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce > Fi

Re: [Freesurfer] topological defect error

From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl Sent: Tuesday, December 3, 2019 11:57 AM To: Freesurfer support list Subject: Re: [Freesurfer] topological defect error   it might also be the hemispheres not being separated, hard to tell (although that almost never happens)

Re: [Freesurfer] surfaceholes in aseg.stats

Hi Laurel yes, the lh.orig.nofix is created using the control points and other things, and so the number of holes in it will definitely change if the placement of control points changes cheers Bruce On Thu, 5 Dec 2019, Laurel Quinlan wrote: External Email - Use Caution H

Re: [Freesurfer] topological defect error

it might also be the hemispheres not being separated, hard to tell (although that almost never happens). You can look at the filled.mgz to check this (the hemis should have different labels) On Tue, 3 Dec 2019, Greve, Douglas N.,Ph.D. wrote: Look at the lh.orig.nofix and see if you can find t

Re: [Freesurfer] Using pre-segmented results

Hi Jordi yes, this should be possible. You might need to run recon-all in stages though. Although if you set the wm.mgz values from SPM to 255 and 1 (not 0) recon-all should detect them as "edits" and retain them cheers Bruce On Tue, 26 Nov 2019, Jordi Huguet wrote: External Emai

Re: [Freesurfer] Is -skullstrip set by default?

Hi Tashrif yes, because then you can just run it by itself (as opposed to part of one of the -autorecon targets) cheers Bruce On Mon, 25 Nov 2019, Billah, Tashrif wrote: > Hi Bruce, > > Thanks for your reply. But then we wouldn't need a -skullstrip option again > given it's on my > default,

Re: [Freesurfer] Is -skullstrip set by default?

Hi Tashrif in case you have data in which the skull has already been stripped. Yes, it is on by default cheers Bruce On Mon, 25 Nov 2019, Billah, Tashrif wrote: > > With recon-all, is > [-skullstrip](https://surfer.nmr.mgh.harvard.edu/fswiki/skullstrip) option > set by > default? > > I am t

Re: [Freesurfer] 4D multi-frame parcellation

it's not delicate - it's just confusing for us when you use it as it refers to a specific dataset cheers Bruce On Mon, 18 Nov 2019, An wrote: External Email - Use Caution Sorry for the confusion, I don't know it has a delicated meaning. I just followed the steps on the frees

Re: [Freesurfer] Fwd: Regarding Issue in reading binary files inside DICOM Directory

sorry, I don't understand what your question is. What are you trying to do? Convert every dicom series in the directory? Convert a single series? On Sun, 17 Nov 2019, sudhakar Mishra wrote: External Email - Use Caution Hi, Sorry for the late reply. As I was asked the questi

Re: [Freesurfer] bias field correction Freesurfer

Hi Adam we do multiple different bias corrections - nu_correct, plus two of our own (mri_ca_normalize and mri_normalize). Is there a reason you don't want to just let recon-all run them in the way it usually does? cheers Bruce On Fri, 15 Nov 2019, Adam Rytina wrote: External Emai

Re: [Freesurfer] Spatial smoothing for cortical folding measures

Hi Yang the size of the smoothing kernel depends on the size of the effect you are looking for (this is called the matched filter theorem), so there is no general smoothing size that is appropriate. We smooth a bit by default for visualization purposes, but you can pick any smoothing size you

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

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 13,

Re: [Freesurfer] Recon all hard failure,

mer > > > 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/

Re: [Freesurfer] Recon all hard failure,

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 co

Re: [Freesurfer] Version 5.3 vs. Version 6

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 > > He

Re: [Freesurfer] Inconsistent Morphology Output

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 through

Re: [Freesurfer] Inconsistent Morphology Output

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 thro

Re: [Freesurfer] flat maps in native space

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, Nasiriavana

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

>> 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

know 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 th

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

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 specif

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

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 straightforwar

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

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 E

Re: [Freesurfer] FreeSurfer transforms

fer. Thanks, Vinny   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

Re: [Freesurfer] FreeSurfer transforms

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 str

Re: [Freesurfer] help

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 voxel

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

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

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 and it will

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

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

...@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, 1

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

ianna 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 wha

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

s recon-all. BW 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

Re: [Freesurfer] recon-all skull stripping

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 no

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

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 C

Re: [Freesurfer] help

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 whi

Re: [Freesurfer] Mri_mask producing only zeros

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 a

Re: [Freesurfer] mri_convert no scaling

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 o

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

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

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, sang

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