Re: [Freesurfer] Fwd: Welcome to the "Freesurfer" mailing list

I think you just did 😊 From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Paolo Zanotti Fregonara Sent: Monday, June 8, 2020 10:39 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Fwd: Welcome to the "Freesurfer" mailing list External Email - Use Caution Hi Would it

Re: [Freesurfer] Splitting surface overlay into separate files

You could also do it pretty easily in matlab or python Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Friday, June 12, 2020 10:44 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Splitting surface overlay into separate files When yo

Re: [Freesurfer] Splitting surface overlay into separate files {Disarmed}

Hi Mason You should be able to load the overlay and the ROIs into matlab, then pick out the vertices in each ROI from the overlay and save them separately. Just be careful about the one-based indexing in matlab. That is, if your ROI is in a label file and you read the vertex indices from it, yo

Re: [Freesurfer] recon-all hanging, how to examine defect

Hi Ken If it is hanging trying to correct a defect it usually means the defect is large. This is typically the case when something else has gone wrong (skull stripping left stuff around, aseg failure, or pathology in the brain). There is a tutorial on checking for defects on our wiki https://s

Re: [Freesurfer] Splitting surface overlay into separate files {Disarmed}

arvard.edu>> on behalf of "Fischl, Bruce" mailto:bfis...@mgh.harvard.edu>> Reply to: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Saturday, 13 June 2020 at 03:02 To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re

Re: [Freesurfer] Splitting surface overlay into separate files {Disarmed}

:wells...@caerdydd.ac.uk> Ffôn: 02920 879628 From: mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of "Fischl, Bruce" mailto:bfis...@mgh.harvard.edu>> Reply to: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Date: Monday, 15 June 2020

Re: [Freesurfer] Correcting recon-all output (missing parts in pial surface)

response. The yellow line is the pial surface. Best, Michael Fischl, Bruce mailto:bfis...@mgh.harvard.edu>> schrieb am Mi., 17. Juni 2020, 21:12: Hi Michael Yes, that should work. Is the surface you are showing below the white or pial? Hopefully the pial (using the color we typically use f

Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format

mri_surf2surf will do it, but you are probably better off going directly to fsaverage rather than downsampling and upsampling cheers Bruce -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Tim Schäfer Sent: Friday, June 19, 2020 9:00 AM To: Freesurfer support

Re: [Freesurfer] Visualization of FreeSurfer overlays in the HCP format

In general almost all of our binaries will read or write almost all formats we support. There are some exceptions to this, but it is generally true Cheers Bruce -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Katsumi, Yuta Sent: Friday, June 19, 2020 9:42 A

Re: [Freesurfer] Brodmann area labels

Hi Peng I think 'lh.BA3b_exvivo.label' is the label you want. The _exvivo just means that the data that went into the prediction was acquired on ex vivo brains. Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Peng Liu Sent: Wednesday, June 24, 2020 7:38 AM To: Freesurfer

Re: [Freesurfer] Brodmann area labels

Bruce, I have tried this label, but it seems not working as it should be. That is why I wanted to create labels like before. Thank you so much! PL On Wed, 24 Jun 2020 at 16:58, Fischl, Bruce mailto:bfis...@mgh.harvard.edu>> wrote: Hi Peng I think 'lh.BA3b_exvivo.label' is th

Re: [Freesurfer] Brodmann area labels

gt; mailto:claudialiu1...@gmail.com>> wrote: > > > External Email - Use Caution > > I usually convert BA3b.label to a nifti mask with SPM to perform ROI > analysis. But with exvivo label, the mask seems not working. > > Many Thanks > > PL >

Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

HI Angela Can you send us the complete command line and screen output of the commands you ran that worked and the ones that failed? Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Angela Favaro Sent: Sunday, June 28, 2020 8:03 AM To: Freesurfer support list Subject: [F

Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

117.1363 -0. -0. -0. 1. Il giorno 28 giu 2020, alle ore 17:51, Fischl, Bruce mailto:bfis...@mgh.harvard.edu>> ha scritto: HI Angela Can you send us the complete command line and screen output of the commands you ran that worked and the ones

Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

. -0. 125.4781 0. -0. -1.95.6241 0. 1. -0. 117.1363 -0. -0. -0. 1. Il giorno 28 giu 2020, alle ore 20:45, Fischl, Bruce mailto:bfis...@mgh.harvard.edu>> ha scritto: Are you s

Re: [Freesurfer] ERROR: input(s) cannot have multiple frames!

.1363 -0. -0. -0. 1. Il giorno 28 giu 2020, alle ore 20:45, Fischl, Bruce mailto:bfis...@mgh.harvard.edu>> ha scritto: Are you sure 102.mgz is from our analysis previously? We typically name the volumes 001.mgz, 002.mgz, etc…. From: freesurfer-boun...@nmr.mgh.

Re: [Freesurfer] Lesioned hemisphere

What is the error? You should be able to run through to the surface generation, then only run the hemi you want Cheers Bruce -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Alina Rojas Sent: Monday, July 6, 2020 10:22 AM To: freesurfer@nmr.mgh.harvard.edu S

Re: [Freesurfer] Lesioned hemisphere

: [Freesurfer] Lesioned hemisphere External Email - Use Caution Hello Bruce, Thanks for the quick answer! I attached the recon-all.log file and a visualization of the subjects problem. How can I run only one hemisphere? Thanks, Alina Am 06.07.2020 um 16:32 schrieb Fischl, Bruce

Re: [Freesurfer] cortical thickness

yes -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Nasiriavanaki, Zahra Sent: Monday, July 6, 2020 12:31 PM To: Freesurfer support list Subject: [Freesurfer] cortical thickness Hi Freesurfer experts I have a question about the way FS calculates cortical t

Re: [Freesurfer] cortical thickness

; On Jul 6, 2020, at 12:40 PM, Fischl, Bruce wrote: > > yes > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > On Behalf Of Nasiriavanaki, Zahra > Sent: Monday, July 6, 2020 12:31 PM > To: Freesurfer support list > Subject: [Fre

Re: [Freesurfer] discontiguous regions assigned to same label by mris_divide_parcellation

Hi Chris If you can upload this subject and let us know exactly which parcels are duplicated we will take a look Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Mcnorgan, Christopher Sent: Saturday, July 11, 2020 1:55 PM To: Freesurfer Mailing List Subject: [Freesurfer

Re: [Freesurfer] The input for FreeSurfer

Hi Hengameh You can try, but 3mm may be too thick for accurate surface models. Once you have too many voxels that contain both sides of a sulcus it is difficult to recover accurate surfaces. Note that our inputs don’t have to be mprage, but 3D acquisitions are highly recommended Cheers Bruce

Re: [Freesurfer] Fwd: Fwd: question regarding mri_vol2label

Hi Julie I don’t think we have anything that will do this out-of-the-box, but it should be easy enough to do in matlab or python. The label files are a text format and we provide .m and .py files to read them. Alternatively you could combine all the labels into a single parcellation file /subje

Re: [Freesurfer] Converting volume to icosahedron surface

Hi Teresa You should be able to load it as an overlay on the fsaverage4 subject. Note that you aren't converting the volume to a surface. Rather you are sampling it onto the surface. Have you run recon-all? Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Tse, Teresa Se

Re: [Freesurfer] FS 7.1.0 - Editing intensity values for WM

Hi Nils There are expert options for this. You can specify things like -min_white 90 to some of the programs like mri_segment and the surface placement stuff Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Nils Böer Sent: Wednesday, July 29, 2020 3:27 PM To: freesurfer@

Re: [Freesurfer] Converting sulc files

Hi Dimitrios Check out the help for mris_convert and replace lh.thickness with lh.sulc (they are in the same 'curv' format) Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Alexopoulos, Dimitrios Sent: Monday, August 3, 2020 6:38 PM To: freesurfer@nmr.mgh.harvard.edu Sub

Re: [Freesurfer] Needing advises for results in my study.

Hi Haewon The problem is that you will never be able to distinguish a scanner effect from a real biological effect since they are in the same subspace. At the very least you should find some control data on both scanners to show that there is no bias in the direction of the effect you are findi

Re: [Freesurfer] Recon-all Soft Errors

er-ow...@nmr.mgh.harvard.edu> When replying, please edit your Subject line so it is more specific than "Re: Contents of Freesurfer digest..." Today's Topics: 1. FS 7.1.0 - Editing intensity values for WM (Nils B?er) 2. Re: FS 7.1.0 - Editing intensity values for WM (Fischl, Br

Re: [Freesurfer] Directories not populating after recon-all

Hi Rohin Can you send us your command line and full screen output? Probably you need to include th e-all directive to recon-all Cheers Bruce -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Rohin Singh Sent: Friday, August 7, 2020 10:11 PM To: freesurfer@nm

Re: [Freesurfer] Recon-all Soft Errors

r-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Fischl, Bruce mailto:bfis...@mgh.harvard.edu>> Sent: Friday, August 7, 2020 9:17:24 AM To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>

Re: [Freesurfer] Available brain atlases in freesurfer in surface format!!

Hi Shreyas Which surface atlas do you mean? We have several and they are stored in different formats. The folding ones are stored as multi-frame spherical tif files, while the parcellations are in an internal format (.gcs). The are all freely available and included with every FreeSurfer install

Re: [Freesurfer] FastSurfer with FreeSurfer version 7.1.0?

Hi Barbara We run a *ton* of tests on thousands of subjects from different scanners and different kinds of pathology before we do a major release. This hasn't been done yet with fastsurfer as it is a huge amount of work Cheers Bruce -Original Message- From: freesurfer-boun...@nmr.mgh.h

Re: [Freesurfer] recon-all output resolution

Yes, that is correct. The "conform" step resamples to 1mm isotropic (among other things) Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Billah, Tashrif Sent: Tuesday, August 25, 2020 10:38 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] recon-all output reso

Re: [Freesurfer] FS educ links

Sure, that is fine From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of John Absher Sent: Tuesday, August 25, 2020 1:00 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] FS educ links External Email - Use Caution Hi, We're implementing freesurfer and other neuroimaging a

Re: [Freesurfer] recon-all error

Hi Jie I would start by looking at your input volume in freeview: freeview -v /usr/local/freesurfer/subjects/2018MPRAGE_p4iso.nii and make sure that the orientation it displays in is correct (that is, that what freeview thinks is anterior/superior/left are indeed those directions). Usually whe

Re: [Freesurfer] How to re-run recon-all

Hi Aldo You should be able to use recon-all -make all ... to run anything that did not complete. You might have to specify the -no-isrunning (or something like that) flag if it didn't terminate cleanly Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Camargo, Aldo Sent:

Re: [Freesurfer] How can I get only aparc+aseg.mgz

Sorry, there is no real shortcut for that - you have to run pretty much everything Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Camargo, Aldo Sent: Friday, August 28, 2020 9:25 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] How can I get only aparc+aseg.m

Re: [Freesurfer] Piriform gyrus and other regions of the olfactory pathway

Hi Diógenes If there are regions that are not in any of our parcellations that you want to obtain measures for, you can manually label them on the fsaverage surface, then use mri_label2label to map them to each individual subject and use mris_anatomical_stats -l to get the measures you want.

Re: [Freesurfer] How to re-run recon-all

8/28/2020 4:26 PM, Camargo, Aldo wrote: External Email - Use Caution Thanks a lot Bruce, Aldo From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> on behalf

Re: [Freesurfer] recon-all error

. Thanks Best, Jie > -原始邮件- > 发件人: "Fischl, Bruce" > 发送时间: 2020-08-27 23:39:20 (星期四) > 收件人: "Freesurfer support list" > 抄送: > 主题: Re: [Freesurfer] recon-all error > > Hi Jie > > I would start by looking at your input volume in freevie

Re: [Freesurfer] recon-all error

Email - Use Caution Here is the snapshot of my freeview window attached. > -Original Messages- > From: "Fischl, Bruce" Sent Time: 2020-08-30 > 02:07:50 (Sunday) > To: "Freesurfer support list" > Cc: > Subject: Re: [Freesurfer] recon-all error >

Re: [Freesurfer] midline to cut the brain stem into Left and Right

That is reasonable From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of ??? Sent: Tuesday, September 1, 2020 12:11 PM To: Freesurfer support list Subject: Re: [Freesurfer] midline to cut the brain stem into Left and Right External Email - Use Caution Thanks! I have a work-around

Re: [Freesurfer] recon-all error

- Use Caution Hi, Bruce I reorineted the views in freesurfer , But the result was wrong again . Please check the figure attached, Is there any problem. BTW, I got the Dicom file, it is .IMA format. How can I use it? Thanks! Jie > -Original Messages- > From: "Fischl, B

Re: [Freesurfer] how to calculate Euler number

Hi Colleen After correction the Euler number should be exactly 2. If it is not, it means the surface is not topologically equivalent to a sphere. Every defect (hole or handle) will decrease it by 2, so an Euler number of -18 (like your lh below) is: # of holes = (2-euler_number)/2 = (2--18)/2

Re: [Freesurfer] how to calculate Euler number

I guess that makes sense -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of C.P.E. Rollins Sent: Thursday, September 3, 2020 12:48 PM To: Freesurfer Subject: Re: [Freesurfer] how to calculate Euler number External Email - Use Caution Thanks fo

Re: [Freesurfer] recon-all error

n-all error External Email - Use Caution Yes , It is the macaque subject from Siemens 7T MRI > -原始邮件- > 发件人: "Fischl, Bruce" > 发送时间: 2020-09-04 00:18:53 (星期五) > 收件人: "Freesurfer support list" > 抄送: > 主题: Re: [Freesurfer] recon-all erro

Re: [Freesurfer] errors in the parcellation

Hi Mariana Can you send us some images with arrows or something so we can see what you mean? Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Mariana Vallejo Azar Sent: Friday, September 4, 2020 6:12 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] errors in t

Re: [Freesurfer] MEMPRAGE vs. MP2RAGE

Hi Caspar Can you elaborate? What are the issues? Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Caspar M. Schwiedrzik Sent: Monday, September 7, 2020 2:27 AM To: Freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] MEMPRAGE vs. MP2RAGE External Email - Use Caution Hi

Re: [Freesurfer] MEMPRAGE vs. MP2RAGE

seem to have built in functionality to deal with the background noise in MP2RAGE, I am wondering whether you still recommend MEMPRAGE over MP2RAGE. I only have regular MPRAGE for comparison at the moment. Thank you, Caspar On Mon, Sep 7, 2020 at 19:56 Fischl, Bruce mailto:bfis

Re: [Freesurfer] Extending the pial surface

Hi Monica We need a bit more detail to figure out why things are going wrong. Can you send screenshots or upload a subject? Is the white matter in that region already 110? Sometimes adding control points in the subjacent wm will bring intensities up enough to correct the pial. You can also chan

Re: [Freesurfer] ERROR | License file for FS 7.1

Hi Otília tkmedit has been deprecated for a long time. Can you try freeview instead? Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Otília C. d'Almeida Sent: Friday, September 11, 2020 8:17 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] ERROR | License file f

Re: [Freesurfer] left-right flip?

And what is your input to recon-all? If it is dicom you should be pretty confident that we will get it correct -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Tuesday, September 15, 2020 10:17 AM To: freesurfer@nmr.mgh.harvard.edu Subj

Re: [Freesurfer] a question on Talairach transformation

Hi Yi LI We compute the registration to MNI but don't apply it. So those images are in native coordinates. Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Yi Li Sent: Tuesday, September 15, 2020 1:08 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] a question

Re: [Freesurfer] [EXTERNAL]Re: a question on Talairach transformation

the em_reg command computes a linear transform to our internal atlas, which is loosely in MNI coords also, but not the official way we support reporting MNI From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Yi Li Sent: Tuesday, September 15, 2020 2:32 PM

Re: [Freesurfer] left-right flip?

e: recon-all -i 1kl5011.nii >> -subjid >> 1kl5011 -all >> >> Is there an efficient way to handle the flipped L-R or should I >> mri_convert the nifti and then do recon-all? >> >> (Assuming that I can't just switch lh_ and rh_ in the >> aparcstats2t

Re: [Freesurfer] left-right flip?

;t just switch lh_ and rh_ in the aparcstats2table) Ellen On 9/15/2020 6:51 PM, Fischl, Bruce wrote: Hi Ellen Can you cc the list so that others can respond? What was your input data? Did you not have dicoms? Cheers Bruce -Original Message- From: Ellen Ji <mailto:ellen...@bli.

Re: [Freesurfer] Prescan normalize and freesurfer

And more details about the study would also help. What field strength? Was the transmit coil a body coil? In the end though I’m not sure we are going to be able to give you an answer as it is an empirical question as to whether including them increases your variance more than it increases your p

Re: [Freesurfer] Prescan normalize and freesurfer

I agree. The 8 channel coils can be trouble as they usually don’t have very good SNR at the vertex, so you are likely to see a lot of variance in the results in those regions Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Glasser, Matthew Sent: Thursday, September 17,

Re: [Freesurfer] Prescan normalize and freesurfer

I would guess it is pretty important for a 12 channel also, although it depends on field strength and also needs a body coil transmit to be maximally effective. In general we use it whenever we can Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Glasser, Matthew Sent: T

Re: [Freesurfer] mri_nu_correct.mni, mri_normalize extremely dark output

I don’t think adding 100 will work as once it scales everything down that far you only have a couple of bits of representation in the conformed ( 1 byte/voxel) images. Maybe someone else can comment on fixing nu_correct? From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Caspar M. Schwi

Re: [Freesurfer] papers that have reported results using FS5.2

The issue was that some code was inserted into the surface deformation algorithm that helped the Wash U HCP images, but made the surfaces quite inaccurate on many other acquisitions. Are there actually papers that used it? I think we found the issue within a couple of weeks and retracted the ver

Re: [Freesurfer] Fwd: non-white matter hypointensity

Yes, they are typically in gray matter, although I’m not sure we see them very often (sometimes in the basal ganglia I think) From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of L Sent: Friday, September 18, 2020 11:28 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Fwd: non-

Re: [Freesurfer] Make BEM with corrected brainmask

Try: mris_expand lh.brainmask.surf 3 inner_skull From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Kadwani, Manorama Sent: Friday, September 18, 2020 6:16 PM To: Freesurfer support list Subject: Re: [Freesurfer] Make BEM with corrected brainmask I read that the option "-thickness" exp

Re: [Freesurfer] Masking surface overlays and spatial correlations {Disarmed}

Hi Mason mri_mask takes volumes as inputs, not label files. If you bring up your volumes and the mask looks in the right place in freeview then it should work cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Mason Wells Sent: Tuesday, September 22, 2020 8:50 AM To: frees

Re: [Freesurfer] Masking surface overlays and spatial correlations {Disarmed}

-bost: wells...@caerdydd.ac.uk<mailto:wells...@caerdydd.ac.uk> Ffôn: 02920 879628 From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Fisc

Re: [Freesurfer] parameterization template and the vertex correspondence in the pial surface

Hi Pam, 1. The variance downweights features that are variable across subject, and let’s the registration depend on more stable features like central/calcarine/sylvian in a smooth manner. 2. The surfaces for a given hemisphere all have the same topology (# of vertices,edges,faces) and ve

Re: [Freesurfer] parameterization template and the vertex in the pial surface

Hi Pam Yes, that’s pretty accurate. Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Pam Garcia Sent: Thursday, September 24, 2020 9:40 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] parameterization template and the vertex in the pial surface

Re: [Freesurfer] parameterization template and the vertex in the pial surface

Yes, that’s true. We compute the vertex correspondence across subjects, but don’t remap the surfaces as we like to keep uniform sampling in the subject space where we can Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Friday, September 25, 2020 9

Re: [Freesurfer] mri_extract issue

Hi Jie Can you clarify what you mean by “head info. Disappeared in a sagittal slice”? Do you mean the head was cropped? If so, that probably just means you have to adjust the fov that you are cropping if you can. Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Jie Zhao

Re: [Freesurfer] mri_extract issue

was cropped.How can I adjust the FOV? My command line is: mri_convert -i orig.mgz -o origfinal.mgz --crop 160 160 160 --conform –nc Thanks! Jie -原始邮件- 发件人:"Fischl, Bruce" mailto:bfis...@mgh.harvard.edu>> 发送时间:2020-09-26 23:31:33 (星期六) 收件人: "freesurfe

[Freesurfer] postdoc opening with Thomas Yeo

Thomas Yeo is looking for a postdoc with a PhD in neuroscience, psychology or related field. Start date is any time in 2021. Topics are quite flexible. More details can be found here: https://sites.google.com/view/yeolab/jobs Contact Thomas if you are interested. Cheers Bruce _

Re: [Freesurfer] License Management

Hi Paul we don't really do much enforcement of the licenses, but it is important to our ability to get the resources to continue to maintain FreeSurfer that our license count reflects the size of our user base. So it would be great if you could request the number of licenses that accounts for y

Re: [Freesurfer] Regarding sMRI scans alignment

Hi Rahul can you explain a bit more what you want? Is this the same subject imaged multiple times? Is it with the same sequence? cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Rahul Sharma Sent: Saturday, October 10, 2020 3:16 AM To: F

Re: [Freesurfer] Regarding sMRI scans alignment

Cheers Bruce From: Rahul Sharma Sent: Sunday, October 11, 2020 3:59 PM To: Freesurfer support list ; Fischl, Bruce Subject: Re: [Freesurfer] Regarding sMRI scans alignment External Email - Use Caution Dataset is taken from ADNI for Alzheimer's Disease Diagnosis. Subjects are diff

Re: [Freesurfer] Fixing error with pial surface

Hi Julie It’s hard to tell from the single slice. Is there white matter in the wm.mgz that doesn’t have surface (?h.white) covering it? That would indicate a topological defect. If you upload the entire gzipped and tarred subject’s directory we will take a look Cheers Bruce From: freesurfer-

Re: [Freesurfer] Fixing error with pial surface

attachment (see the red cursor). Also I have added the first (coronal) slice that starts to show white matter (couple slices later). Let me know if you still would like me to upload the data. Best Julie On Mon, 12 Oct 2020 at 14:23, Fischl, Bruce mailto:bfis...@mgh.harvard.edu>> wrote: Hi

Re: [Freesurfer] Error during skullstripping: numerical result out of range

Hi Julia Can you check the output of the skull stripping and see if it failed? Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Hye Min Shin Sent: Tuesday, October 20, 2020 1:13 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] Error during skullstripping: numer

Re: [Freesurfer] Error running mris_ca_label

You are missing a switch before the ../label/lh.cortex.label parameter (-l I think? Read the help). That makes all the positional parameters apparently in the wrong place From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Rollo, Patrick Sent: Tuesday, October 20, 2020 11:06 AM To: frees

Re: [Freesurfer] please help me

Hi Saman Recon-all will give you a comprehensive assessment of most macroscopically visible structures in the brain. You don’t have to convert to nifty first – just point recon-all at a single slice in the proper dicom series (for your 3D T1-weighted scan), and it will spend a few hours doing s

Re: [Freesurfer] please help me

morphology features and in step2 create a deep learning model that predict age. According to what I said, what should I do? If I have to use recon-all with what code can I do this? And what is the use of nifty? On Wednesday, October 21, 2020, 1:06:50 AM GMT+3:30, Fischl, Bruce mailto:bfis

Re: [Freesurfer] The non-existent field'numEntries' is referenced.(write_annotation.m)

Where did you get the ct from? From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of 1248742467 Sent: Thursday, October 22, 2020 7:25 AM To: freesurfer Subject: [Freesurfer] The non-existent field'numEntries' is referenced.(write_annotation.m) External Email - Use Caution hello,

Re: [Freesurfer] please help me

mailto:smnfoul...@yahoo.com>> wrote: hi Bruce thank you very very much On Wednesday, October 21, 2020, 9:05:36 PM GMT+3:30, Fischl, Bruce mailto:bfis...@mgh.harvard.edu>> wrote: Nifty is a format that a lot of people use (including us) but it is not needed for our processing. Pick *one*

Re: [Freesurfer] please help me

It depends on your hardware. On a modern multi-core CPU you can get it down to 3-4 hours I believe, and I think the final message is something like “recon-all finished in…” Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of saman fouladi Sent: Friday, October 23, 2020 4:12

Re: [Freesurfer] (no subject)

Sorry, that is not a question for us but rather for your local sys admin From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of saman fouladi Sent: Friday, October 23, 2020 6:52 AM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] (no subject) External Email - Use Caution hi

Re: [Freesurfer] please help me

Which output can I use to predict age after recon-all? On Friday, October 23, 2020, 11:46:09 PM GMT+3:30, saman fouladi mailto:smnfoul...@yahoo.com>> wrote: yes and replacing -sdir with -sd thank you very much On Friday, October 23, 2020, 5:58:11 PM GMT+3:30, Fischl, Bruce mailt

Re: [Freesurfer] please help me

and got a little confused. Can you help me a little if you have any information? On Saturday, October 24, 2020, 6:04:07 PM GMT+3:30, Fischl, Bruce mailto:bfis...@mgh.harvard.edu>> wrote: Hi Saman That’s really a scientific question and up to you! Bruce From: freesurfe

Re: [Freesurfer] Problem with pial and white matter segmentation

Hard to say for sure, but I would guess you have an incorrectly fixed topological defect in that region. Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Edoardo Pinzuti Sent: Wednesday, October 28, 2020 7:02 AM To: Freesurfer support list Subject: [Freesurfer] Problem w

Re: [Freesurfer] Statistic Difference Region on the Fsaverage Turned into No Statistic Difference after Mapping onto the Subjects

The segmentation nets typically output one-hot encoded values. So if you have 30 labels, the output layer has 30 outputs, which can be loosely interpreted as p-values for each label (they will add to 1). To turn it into a segmentation you take the argmax over the 30-label dimension and toss the

Re: [Freesurfer] Fixing error with pial surface {Disarmed}

lly changed. ftp> put subject_FS_upload.zip local: subject_FS_upload.zip remote: subject_FS_upload.zip 421 Service not available, remote server has closed connection Could you help me out with this? Thanks Julie On Mon, 12 Oct 2020 at 15:48, Fischl, Bruce mailto:bfis...@mgh.harvard.edu>> wro

Re: [Freesurfer] Different Sequences Longitudinal Stream {Disarmed}

Hi Lee It's really hard to say. The change in voxel size might sound trivial, but it is a 30% change in volume (and hence SNR). The longer TE will counteract that by increasing T2* weighting. Sorry I don't have anything more conclusive to say except that it is obviously not ideal Bruce From: f

Re: [Freesurfer] Recon1 command

HI Kelli It sounds like you started running at some point but didn't get very far? Try something like: mv /home/blah/blah/blah/1234 /home/blah/blah/blah/saved.1234 recon-all -subjid 1234 -i 1234.nii -autorecon1 and see if that works (then you can probably delete the saved.1234 dir if you want)

Re: [Freesurfer] Subcortical Segmentation Atlas Question

Hi Tyler The atlas is described in our 2002 (Neuron) and 2004 (NeuroImage) papers. It implements the anisitropic, nonstationary Markov Random Field segmentation. I think lots of people have compared their segmentations to it, although I would urge some caution as many of them are biased IMO (e.

Re: [Freesurfer] Editing Issues

Hi Harriet Do you know that it is a hole? More likely is that it only looks like one on a single slice and if you scroll back and forth or change to a different view you will find that it is not actually a hole. As for the second question you only need to edit things if the nearby surfaces are

Re: [Freesurfer] Mean thickness estimation

Hi Stephanie By using the average/std within region, then averaging those, you are weighting small regions more. I would just use the average/std across cortex. Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Stephanie K Sent: Wednesday, November 18, 2020 12:24 PM To: f

Re: [Freesurfer] Mean thickness estimation

Hi Stephanie I think that is always a good idea, unless for some reason it isn’t possible Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Stephanie K Sent: Thursday, November 19, 2020 2:14 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Mean thickness es

Re: [Freesurfer] Mean thickness estimation {Disarmed}

inspected as a further data cleaning step? I really appreciate your help. Thanks On Thu, Nov 19, 2020 at 3:55 PM Fischl, Bruce mailto:bfis...@mgh.harvard.edu>> wrote: Hi Stephanie I think that is always a good idea, unless for some reason it isn’t possible Cheers Bruce From: freesurfe

Re: [Freesurfer] Mean thickness estimation {Disarmed}

measures (thickness of mean hemisphere, estimated intracranial volume) as the data had been processed and removed from further Freesurfer processing if they had severe artifacts or irregularities. Many thanks for your advice. On Thursday, November 19, 2020, Fischl, Bruce mailto:bfis

Re: [Freesurfer] Mean Curvature for whole hemisphere

Hi Josue No real reason. We provide maps of the mean curvature so it would be easy enough to average them. Not sure it will have much meaning. I guess it will loosely measure how much folding there is (since the less folding the more sphere-like the geometry will become) Cheers Bruce From: fr

Re: [Freesurfer] Mean Curvature

Hi Letitia I wouldn't think so since mean curvature is a differential property and so should be pretty local, but I guess controlling for overall curvature would be a slightly different hypothesis Cheers Bruce From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Letitia Schneider Sent:

Re: [Freesurfer] Freesurfer skullstripping error

Hi Yezhe It depends a lot on what your resolution, read out direction, bandwidth and field strength are. We generally fix these with T2 or FLASH scans at the same resolution/geometry/readout as the T1. Otherwise they are pretty tough as the dura is close enough to the gray matter that you can’t

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