Re: [Freesurfer] FS 6.0 outputs for use with 7.2 Tracula

External Email - Use Caution Posting again. Can FS6.0 structural outputs (i.e. aparc+aseg) be used as inputs for running Tracula version in FS 7.2? Jim From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Alexopoulos, Dimitrios Sent: Friday, December 15, 2023 3:35 PM

Re: [Freesurfer] FS 6.0 outputs for use with 7.2 Tracula

External Email - Use Caution Sorry, posting again for FS experts. Jim From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Alexopoulos, Dimitrios Sent: Tuesday, December 12, 2023 4:23 PM To: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] FS 6.0 outputs for use

[Freesurfer] FS 6.0 outputs for use with 7.2 Tracula

External Email - Use Caution Can the tracula version in FS 7.x be used with surface outputs generated with FS 6.0? Our segmentations/surfaces generated with 6.0 look good but we'd like to generate the 42 WM pathways incorporated in FS 7x. Is this possible? I was under the

[Freesurfer] tracula using FS 7.2

External Email - Use Caution We'd like to use FS7.2 to generate hi-re surfaces on 0.8mm data on 6yo subject. However, we'd like to be able to generate the white matter tracts that are produced with older versions (specifically 6.0), not the new 42 tracts with 7.2. Can a FS 6.0

[Freesurfer] ANTs denoising

External Email - Use Caution To which anatomical volume is ANTs denoising applied to for generating the orig surface? We do ANTS denoising to the input T1 before running recon-all and were wondering if we are denoising our data twice. Thx. Jim

Re: [Freesurfer] re-running recon-all after aseg.presurf.mgz edits

-created with these two options. So, not sure about ?h.aparc.stats. Best, Yujing From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> On Behalf Of Alexopoulos, Dimitrios Sent: Thursday, June 29,

[Freesurfer] re-running recon-all after aseg.presurf.mgz edits

External Email - Use Caution A few quick questions FS experts. I made manual edits on subcortical structures in outputs from FS6.0. Specifically, I made the edits on the aseg.presurf.mgz file. I then reran using: recon-all -s neo267e_nil -autorecon2-noaseg -autorecon3 Do the

Re: [Freesurfer] using FS7.2 tracula with FS6.0 outputs

Of Alexopoulos, Dimitrios Sent: Friday, December 02, 2022 10:55 AM To: Freesurfer support list Subject: [Freesurfer] using FS7.2 tracula with FS6.0 outputs * External Email - Caution * External Email - Use Caution HI, we have run a cohort of 200 subjects through FS6.0 (including tracula

[Freesurfer] using FS7.2 tracula with FS6.0 outputs

External Email - Use Caution HI, we have run a cohort of 200 subjects through FS6.0 (including tracula) with good results. Is it possible to use the FS6.0 outputs (aparc+aseg, etc.) to run these data though only the updated tracula pipeline in 7.2? Jim

Re: [Freesurfer] volumes/surfaces FS6.0 vs FS7.2/3.2

r-boun...@nmr.mgh.harvard.edu>> on behalf of Alexopoulos, Dimitrios mailto:dimitriosalexopou...@wustl.edu>> Sent: Friday, November 4, 2022 5:20 PM To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] volumes/surfaces FS6.0 vs FS7.2/3.2 External

[Freesurfer] volumes/surfaces FS6.0 vs FS7.2/3.2

External Email - Use Caution We have processed a large pediatric cohort (9-10 y.o. subjects) acquired with 1 mm isotopic voxels using FS 6.0. We are now beginning to rescan the same cohort at 15-16 y.o. using the exact same imaging protocol and scanner (3T, Prizma). If we

[Freesurfer] 7.2.0 CentOS7 and Ubuntu 18.04

External Email - Use Caution We've made system software upgrades recently and of some our data was run using the FS 7.2.0 CentOS 7 build but on Ubuntu 18.04 servers. The outputs look good and there no output errors. Should these data be rerun? Jim

[Freesurfer] forcing use of ants-n3 with FS 7.2

External Email - Use Caution Just want to confirm the following change is good to use to force use of ants-n3 with FS 7.2. It appears as though FS 7.2 with ants-n3 gives us better results than the default n4. We changed /etc/recon-config.yaml to the following, and it appears

[Freesurfer] accumbens nucleus volumes

External Email - Use Caution The accumbens nucleus is very difficult to delineate in some younger (3yo) subjects and in infants run through the infant pipeline. The pipelines segment the region but I'm not sure how reliable the volume measures are. Can the accumbens volume be

[Freesurfer] error estimates in FS total brain volumes

External Email - Use Caution Hi all, What is a reasonable estimate of the error margin in the total brain volume estimates of Freesurfer? Is there a reference that discusses this? Jim The materials in this message are private and may contain

Re: [Freesurfer] rerunning on 7.2 with edited brainmask using hi-res

External Email - Use Caution Can someone confirm? Thx. Jim From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Alexopoulos, Dimitrios Sent: Tuesday, April 12, 2022 3:24 PM To: Freesurfer support list Subject: [Freesurfer] rerunning on 7.2 with edited brainmask using hi

[Freesurfer] rerunning on 7.2 with edited brainmask using hi-res

External Email - Use Caution We are running some hi-res 0.8mm3 isotropic data through FS 7.2 using the following command. recon-all -s subj -all -hires We are adding back brain which has been removed by the masking process by cloning the T1/brainmask images in freeview and

Re: [Freesurfer] error with trac-all -prep in FS7.2 tracula

External Email - Use Caution Hi all, any comments related to these errors we get with trac-all -prep in FS 7.2? Thanks. Jim From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Alexopoulos, Dimitrios Sent: Friday, February 25, 2022 2:05 PM To: Freesurfer support list

[Freesurfer] error with trac-all -prep in FS7.2 tracula

External Email - Use Caution Hi all, We are reprocessing some of our data with FS 7.2 to evaluate the new updates to Tracula, however, we are getting errors from the trac-all -prep -c configfile step. The last 20 lines of output are shown below. Anyone have any comments on how

[Freesurfer] editing the aseg.mag using another tool and then rerunning

External Email - Use Caution A quick question. Is it feasible or even possible to edit the aseg.mgz using another program (i.e. ITK-snap after converting to nifti), and rerunning the pipeline using the revised aseg as input To regenerate volumes and surfaces? Do WM edits need

Re: [Freesurfer] Using only a aparc+aseg input file for TRACULA

fer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Alexopoulos, Dimitrios mailto:dimitriosalexopou...@wustl.edu>> Sent: Thursday, October 21, 2021 2:59 PM To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject

Re: [Freesurfer] Using only a aparc+aseg input file for TRACULA

TRACULA turns out to be to various types of snafus. So it's worth trying. From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Alexopoulo

Re: [Freesurfer] Using only a aparc+aseg input file for TRACULA

suggested below? Jim From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Alexopoulos, Dimitrios Sent: Thursday, October 21, 2021 5:08 PM To: Freesurfer support list Subject: Re: [Freesurfer] Using only a aparc+aseg input file for TRACULA * External Email - Caution * External Email

Re: [Freesurfer] Using only a aparc+aseg input file for TRACULA

-aseg aseg.mgz -o aseg_CCseg.mgz $subj) to get the CC lables. Lilla From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Alexopoulos, Dimitrios Sent: Thursday, October 21, 2021 2:59 PM To: Freesurfer support list Subject: Re: [Freesurfer] Using only a aparc+aseg

Re: [Freesurfer] Using only a aparc+aseg input file for TRACULA

with the accuracy of the tracts that terminate or neighbor the thalamus. Anastasia. From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Alexopoulo

Re: [Freesurfer] Using only a aparc+aseg input file for TRACULA

; on behalf of Alexopoulos, Dimitrios mailto:dimitriosalexopou...@wustl.edu>> Sent: Wednesday, October 20, 2021 2:54 PM To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] Using only a aparc+aseg input file for TRACULA External Email - Use C

[Freesurfer] Using only a aparc+aseg input file for TRACULA

External Email - Use Caution Hi, It was my understanding that TRACULA only uses the aparc+aseg segmentation from the standard structural output from FS 7.1.1., and specifically for the relative positions (left, right, anterior, etc.) of each tract with respect to the

Re: [Freesurfer] WM or Pial edits to correct surfaces

not extend far enough. This is due to the WM strands being very thin and partial voluming with GM. The fix for this is to edit the wm.mgz and rerun recon-all with -autorecon-wm -autorecon3. doug On 5/27/2021 2:19 PM, Alexopoulos, Dimitrios wrote: External Email - Use Caution External

[Freesurfer] Tracula 7.2 using older structural outputs

External Email - Use Caution HI, Can you run Tracula 7.2 using older structural outputs generated with FS 6.0 and 7.1.1? Jim The materials in this message are private and may contain Protected Healthcare Information or other information of a

[Freesurfer] Total WM surface area

External Email - Use Caution Hi, Are the total lh/rh cortical surface areas in stats/aparc.stats = parcel1 surface area + parcel2 surface area…? Get Outlook for

[Freesurfer] FW: WM or Pial edits to correct surfaces

run using recon-all -s subject -expert yourexpertoptions.txt -pial -lh Jim From: Alexopoulos, Dimitrios Sent: Friday, May 28, 2021 1:08 PM To: Freesurfer support list Subject: RE: [Freesurfer] WM or Pial edits to correct surfaces Thanks Doug. Will try with difference distances. Where

Re: [Freesurfer] WM or Pial edits to correct surfaces

The above command will run just the pial of just the lh hemi, so you should have your answer in a few minutes On 5/27/2021 2:19 PM, Alexopoulos, Dimitrios wrote: External Email - Use Caution External Email - Use Caution Hi users, We're having some issues with running some of

[Freesurfer] WM or Pial edits to correct surfaces

External Email - Use Caution Hi users, We're having some issues with running some of our 2-3yo data (0.8mm isotropic) through FS7 with and without the -hires flag. There are persistent issues with the frontal lobe regions where the pial has not extended to outer surface as

Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.

conf2hires? Jim From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Friday, March 19, 2021 11:09 AM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] -hires vs -conf2hires in 7.1.1. * External Email - Caution * On 3/19/2021 12:03 PM, Alexopoulos, Dimitrios

Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.

of my time looking at surface placement in high res. In the end, I don't think it would make much of a difference as the subcortical structures are fairly low-res to begin with. On 9/9/2020 11:02 AM, Alexopoulos, Dimitrios wrote: External Email - Use Caution Ok. Looks like the updated

Re: [Freesurfer] rerunning FS 7.1.1 after brainmask.mgz edits

, Alexopoulos, Dimitrios wrote: External Email - Use Caution Thnaks. Some of the data may have been copied from different places so I'm concerned the time stamps might not be accurate which is why I'd prefer to run from scratch using recon-all -s -i -hires -all Nothing else is needed

Re: [Freesurfer] rerunning FS 7.1.1 after brainmask.mgz edits

* External Email - Caution * That is fine. You could save a few min by not starting from scratch, but the brainmasking happens very close to the beginning. On 2/17/2021 3:57 PM, Alexopoulos, Dimitrios wrote: External Email - Use Caution Hi, We are finding that the skull-stripping in standard

[Freesurfer] rerunning FS 7.1.1 after brainmask.mgz edits

External Email - Use Caution Hi, We are finding that the skull-stripping in standard FS 7.1.1. in a few of our 3yo subjects is a little aggressive and is removing brain from the brainmask primarily in the occipital pole region. We decided to use the "cloning to T1 method",

[Freesurfer] Fwd: Freesurfer edits

External Email - Use Caution Any comments from FS users to best best tackle these manual edits? Jim Get Outlook for Android<https://aka.ms/ghei36> From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Alexopoulos, Dimitrios Sent: T

Re: [Freesurfer] Freesurfer edits

_ From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Alexopoulos, Dimitrios Sent: Tuesday, October 20, 2020 11:24 AM To: Freesurfer support list Subject: [Freesurfer] Freesurfer edits External Email - Use Caution Hi freesurfer editing experts. Below are snapshots of the brainmask

[Freesurfer] Freesurfer edits

External Email - Use Caution Hi freesurfer editing experts. Below are snapshots of the brainmask, aseg and wm.mgz for a 2 year old run through FS 7.1.1 I'm hoping for feedback on the best way to make the relevant edits to the three blue-circled regions. 1. In the

Re: [Freesurfer] Tracula FS 6 vs FS 7.1.1

r-boun...@nmr.mgh.harvard.edu>> on behalf of Alexopoulos, Dimitrios mailto:dimitriosalexopou...@wustl.edu>> Sent: Thursday, September 17, 2020 1:22 PM To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Freesurfer] Tracula FS 6 vs FS 7.1.1 External Emai

Re: [Freesurfer] Tracula FS 6 vs FS 7.1.1

eesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Alexopoulos, Dimitrios mailto:dimitriosalexopou...@wustl.edu>> Sent: Thursday, September 17, 2020 12:47 PM To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: Re: [Fr

Re: [Freesurfer] Tracula FS 6 vs FS 7.1.1

r-boun...@nmr.mgh.harvard.edu>> on behalf of Alexopoulos, Dimitrios mailto:dimitriosalexopou...@wustl.edu>> Sent: Tuesday, September 15, 2020 5:04 PM To: Freesurfer support list mailto:freesurfer@nmr.mgh.harvard.edu>> Subject: [Freesurfer] Tracula FS 6 vs FS 7.1.1 External Email - Us

[Freesurfer] Tracula FS 6 vs FS 7.1.1

External Email - Use Caution Are there any differences in usage /outputs from Tracula in FS 6 vs FS 7.1.1? Specifically as it relates to the customized dmrirc config file? The wiki mentions a beta version of Tracula in FS. 7.2. Will the general usage be similar to 6/7.1.1?

Re: [Freesurfer] mean gyrification index

External Email - Use Caution Try this for the left hem. This command includes the excludeid = 0 mri_segstats --slabel subject_ID lh $SUBJECTS_DIR/subject_ID/label/lh.cortex.label --i $SUBJECTS_DIR/subject_ID/surf/lh.pial_lgi --excludeid 0 --sum lh.aparc.pial_lgi_lh.stats

Re: [Freesurfer] mean gyrification index

...@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Wednesday, September 09, 2020 12:13 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] mean gyrification index * External Email - Caution * I think that should work On 9/9/2020 12:59 PM, Alexopoulos, Dimitrios wrote

Re: [Freesurfer] mean gyrification index

External Email - Use Caution I have used this for mean GI per hemisphere: mri_segstats --i lh.lgi.mgz --slabel subject lh $SUBJECTS_DIR/subject/label/lh.cortex.label --excludeid 0 --o lh.lgi.sum Jim From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve

Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.

think it would make much of a difference as the subcortical structures are fairly low-res to begin with. On 9/9/2020 11:02 AM, Alexopoulos, Dimitrios wrote: External Email - Use Caution Ok. Looks like the updated -hires might be the better option overall. Anecdotally, wouldn't you

Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.

lution images. I'm not sure whether volume segmentation (ie, aseg) of highres images is better than at 1mm. On 9/9/20 10:30 AM, Alexopoulos, Dimitrios wrote: External Email - Use Caution Falk and Doug, thx for clarifying. Before we begin processing a new cohort using 7.1, I want to make

Re: [Freesurfer] -hires vs -conf2hires in 7.1.1.

e to test v7 intensively, though. Hope this helps. Best, Falk Von: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> <mailto:freesurfer-boun...@nmr.mgh.harvard.edu> Im Auftrag von Alexopoulos, Dimitrios Gesendet: Mittwoch, 9. September 2

[Freesurfer] -hires vs -conf2hires in 7.1.1.

External Email - Use Caution Does the hires flag still generate segs at the native hi resolution and place surfaces on the 1mm volumes, whereas conf2hires generates volumes at 1mm but places surfaces on the hires images? Which option is recommended and why? Jim Get Outlook

Re: [Freesurfer] use of ANTs Denoising in FS 7.1

ltered brain.mgz but using the orig surface created with the denoised brain.mgz. So the denoising helps to create the orig surface which is then used to initialize the final surfaces. On 8/25/2020 5:37 PM, Alexopoulos, Dimitrios wrote: External Email - Use Caution I’m looking t

Re: [Freesurfer] use of ANTs Denoising in FS 7.1

smoothing of any kind has the potential to bias the surface placement so we recommend against denoising the input. On 8/25/2020 4:56 PM, Alexopoulos, Dimitrios wrote: External Email - Use Caution Hi all, In previous datasets, and prior to FS 7, we independently ran ANTs denosing on the input

[Freesurfer] use of ANTs Denoising in FS 7.1

External Email - Use Caution Hi all, In previous datasets, and prior to FS 7, we independently ran ANTs denosing on the input T1s prior to running recon-all, However, FS 7.1 now appears to use the denosing utility in parts of the pipeline. "ANTS denoise is used when creating

Re: [Freesurfer] FS edits of subcortical parcels

V6 run recon-all -s subject -autorecon2 -nogcareg -nocanorm -nocareg -autorecon3 I would suggest doing a test on one subject to make sure that the edits get propagated properly. This is not the kind of thing we do that often, so use caution. On 8/17/2020 12:59 PM, Alexopoulos, Dimitrios

Re: [Freesurfer] FS edits of subcortical parcels

] FS edits of subcortical parcels * External Email - Caution * Copy aseg.auto.mgz to aseg.manedit.mgz, then edit aseg.manedit.mgz. If you are using v7, then you can run recon-all -s subject -autorecon2-samseg -autorecon3 On 8/13/2020 5:35 PM, Alexopoulos, Dimitrios wrote: External Email

[Freesurfer] fs7..1.1 and age range

External Email - Use Caution Is 7.1.1. still considered to be best used as a pipeline for subjects older than ~5yo? Have any parts of the infant pipeline been incorporated so that it be used for babies or subjects up to 2yo, or do we still need to run separate infant pipeline?

[Freesurfer] FS edits of subcortical parcels

External Email - Use Caution FS editing experts, I have a subject with enlarged ventricles and processed the subject with recon-all -bigventricles flag. The surfaces look good but the subcortical segmentation and some WM around the ventricles , especially for the right hem,

[Freesurfer] cortical surface area calculation

External Email - Use Caution Hi all, Does this command calculate the Cortical Surface Area without the non-cortical Medial Wall?? mris_calc --label ../label/lh.cortex.label lh.area stats Jim The materials in this message are private and may

Re: [Freesurfer] FW: LGI and Global GI

@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] FW: LGI and Global GI * External Email - Caution * I guess you could use something like mri_segstats --i lh.lgi.mgz --slabel subject lh $SUBJECTS_DIR/subject/label/lh.cortex.label --excludeid 0 --o lh.lgi.sum On 6/28/2020 11:08 AM, Alexopoulos, Dimitrios wrote

[Freesurfer] Local GI vs. Folding Index

External Email - Use Caution The aparc.stats file contains a Folding Index measure for each cortical parcellation. How is this measure determined and how is it different from the one calculated using the -localGI flag after precessing a subject? Jim Get Outlook for

[Freesurfer] Converting sulc files

External Email - Use Caution Is there a command that will convert the ?h.sulc to ascii, i.e. depth at each vertex? Get Outlook for Android The materials in this message are private and may contain Protected Healthcare

[Freesurfer] FW: LGI and Global GI

External Email - Use Caution Is generating a Global hemispheric Gyrification Index possible? From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Alexopoulos, Dimitrios Sent: Wednesday, May 27, 2020 3:39 PM To: Freesurfer support list Subject: [Freesurfer] LGI and Global

[Freesurfer] LGI and Global GI

External Email - Use Caution HI, I have generated the LGI for a group of pediatric subjects. Is there a way to compute a single Global gyrification index measure for each subject? Jim, The materials in this message are private and may contain

Re: [Freesurfer] total brain volume

On Behalf Of Douglas N. Greve Sent: Monday, April 27, 2020 7:02 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] total brain volume * External Email - Caution * Yes, if you exclude the ventricles On 4/27/2020 6:03 PM, Alexopoulos, Dimitrios wrote: External Email - Use

[Freesurfer] total brain volume

External Email - Use Caution Along with normalizing for eTIV, we'd like to normalize regional cortical volumes for total brain/tisuse volume (TBV). Is the output BrainSegNotVent in the aseg.sats basically equivalent to TBV? Jim The materials

Re: [Freesurfer] eTIV vs. ICV

: Friday, December 14, 2018 9:31 AM To: Freesurfer support list Subject: Re: [Freesurfer] eTIV vs. ICV Hi Jim it is an estimate of everything inside skull. cheers Bruce On Thu, 13 Dec 2018, Alexopoulos, Dimitrios wrote: > > External Email - Use Caution > > The eTIV from FS 6

[Freesurfer] eTIV vs. manual ICV

External Email - Use Caution I was just wondering if using the eTIV from FS 6.0 is a reliabile measure for intracanial volume normalization. Typically, manual ICV includes extra-axial CSF which I don't think is included in the eTIV method, correct? Our population is a control

Re: [Freesurfer] medial wall metric file

l.mask.mgz On 1/28/2020 6:31 PM, Alexopoulos, Dimitrios wrote: External Email - Use Caution Is there a freesurfer file that contains metric info that delineates the medial wall in the native surface output for an individual? It appears to be associated with the ?lh.aparc.annot file (below).

Re: [Freesurfer] medial wall metric file

om outside the university. Do you mean you want a binary mask of the medial wall? You can create a mask of the cortical label (?h.cortex.label) with mri_label2label You can then invert that with something like fscalc lh.cortex.mask.mgz not -o lh.medialwall.mask.mgz On 1/28/2020 6:31 PM, A

[Freesurfer] medial wall metric file

External Email - Use Caution Is there a freesurfer file that contains metric info that delineates the medial wall in the native surface output for an individual? It appears to be associated with the ?lh.aparc.annot file (below). I'd like to be able to export the medial wall

Re: [Freesurfer] Version 6.0 patches for hi-res data

1mm. On 1/24/2020 5:17 PM, Alexopoulos, Dimitrios wrote: External Email - Use Caution I came across info for version 6.0 that generated statistical errors when using high resolution input. https://surfer.nmr.mgh.harvard.edu/fswiki/BrainVolStatsFixed We have used the ‘-hires’ flag

[Freesurfer] Version 6.0 patches for hi-res data

External Email - Use Caution I came across info for version 6.0 that generated statistical errors when using high resolution input. https://surfer.nmr.mgh.harvard.edu/fswiki/BrainVolStatsFixed We have used the '-hires' flag and, more recently, the '-conf2hires' flag with

Re: [Freesurfer] recon-all at native resolution

that I pointed to below to get better surfaces. On 10/25/19 12:30 PM, Alexopoulos, Dimitrios wrote: External Email - Use Caution Opps, here are the snapshots. The aseg subcortical look good using either the -hires or -conf2hires flags. The cortical parcellation is not including some ctx

Re: [Freesurfer] recon-all at native resolution

There was no snapshot. Can you resend? On 10/24/2019 7:06 PM, Alexopoulos, Dimitrios wrote: > External Email - Use Caution > > I apologize for the confusion. Whether I use the -hires or -conf2hires flag > the subcortical segmentations look good. > > The cortical segme

Re: [Freesurfer] recon-all at native resolution

On Behalf Of Greve, Douglas N.,Ph.D. Sent: Thursday, October 24, 2019 5:37 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] recon-all at native resolution You mean the surfaces using -hires look fine? If so, then continue to use -hires On 10/24/19 6:32 PM, Alexopoulos, Dimitrios

Re: [Freesurfer] recon-all at native resolution

on the high res volumes, but the aseg will be at 1mm. If you need the aseg at highres, then you will need to use the -hires flag (but the surfaces will suffer) On 10/24/19 2:55 PM, Alexopoulos, Dimitrios wrote: > External Email - Use Caution > > Doug, > > I copied ove

Re: [Freesurfer] recon-all at native resolution

a patch I created for the HCP, see https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp/readme On 10/15/19 12:13 PM, Alexopoulos, Dimitrios wrote: > > External Email - Use Caution > > We have data acquired at 0.8mm isotropic and would like to maintain >

Re: [Freesurfer] recon-all at native resolution

at native resolution better to use a patch I created for the HCP, see https://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/6.0.0-patch/hcp/readme On 10/15/19 12:13 PM, Alexopoulos, Dimitrios wrote: > > External Email - Use Caution > > We have data acquired at 0.8mm isotrop

[Freesurfer] recon-all at native resolution

External Email - Use Caution We have data acquired at 0.8mm isotropic and would like to maintain this resolution in the processing stream rather than FS resampling to 1mm. Is the command to do this 'recon-all -hires -all'? Are there any drawback to doing this? Jim

[Freesurfer] FS6.0 on 2yo subjects

External Email - Use Caution We have acquired 0.8mm isotropic T1-mprage sequences on 2 year old subjects. Although the output looks good (see below), is it recommended to use FS6.0 on a young cohort? [cid:image005.jpg@01D56E40.7241E0E0][cid:image006.jpg@01D56E40.7241E0E0]

Re: [Freesurfer] 001 vs brainmask views in freeview

brainmask views in freeview The first volume is always displayed in its original orientation where pixel data are stored. So that the pixel data don't get resampled (unless you force it with '-r' flag to resample it in standard RAS). Ruopeng On 9/16/19 1:06 PM, Alexopoulos, Dimitrios wrote

Re: [Freesurfer] 001 vs brainmask views in freeview

is nearest-neighbor. Thus you get the blocky look. You can try loading it with trilinear or cubic resampling like this from the command-line: freeview -v 001.mgz brainmask.mgz -trilinear Ruopeng On 9/16/19 12:41 PM, Alexopoulos, Dimitrios wrote: External Email - Use Caution Hi all, I ran

[Freesurfer] 001 vs brainmask views in freeview

External Email - Use Caution Hi all, I ran a 2yo subject through FS6.0 using 'recon-all -i /firstdicom.dcm -all' and the output segmentations and surfaces looks good. Can someone explain why I see different alignments when I view the 001.mgz and brainmask.mgz files in

[Freesurfer] units for tracula output

External Email - Use Caution What units are the diffusion measures generated by tracula that are found in the files named "pathstats.overall.txt". For example, as 10^-3 Jim The materials in this message are private and may contain Protected

[Freesurfer] eTIV vs. ICV

External Email - Use Caution The eTIV from FS 6.0 has been used by many as a normalization measure for regional volumetric analyses. I know it is not a true voxel count but does it conceptually include extra-axial CSF or is it more a total tissue volume? Jim

[Freesurfer] WM edits

External Email - Use Caution I'd like to make edits to correct the superior regions where then pial surface truncates WM (images below). Would it be more useful to use controls points in the WM or add WM to the wm.mgz. Jim

Re: [Freesurfer] /mri/orig/001.mgz vs T1.mgz

, September 12, 2018 2:15 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] /mri/orig/001.mgz vs T1.mgz depends a little bit on the viewer, but we resample into the scanner space, so it could look like it is tilted On 09/12/2018 12:33 PM, Alexopoulos, Dimitrios wrote: > > Ex

[Freesurfer] hippocampus subfields with T2

External Email - Use Caution We have a cohort of 10yo subjects for which we have acquired a 0.85mm isotropic T1-mprage and a 1mm isotropic T2-space. Is it possible or even recommended to try and generate better hippocampal segmentation in fressurfer 6.0 using both the T1 and T2,

Re: [Freesurfer] tractstats2table - all tracts for multiple subjects

_ From: freesurfer-boun...@nmr.mgh.harvard.edu<mailto:freesurfer-boun...@nmr.mgh.harvard.edu> mailto:freesurfer-boun...@nmr.mgh.harvard.edu>> on behalf of Alexopoulos, Dimitrios mailto:dimitriosalexopou...@wustl.edu>> Sent: Tuesday, June 12, 2018 5:08:20 PM To: Fre

[Freesurfer] tractstats2table - all tracts for multiple subjects

External Email - Use Caution Hi, For a group analysis, it possible to use 'tractstats2table' to generate a single table that contains all the tracts for multiple subjects? It's not intuitively obvious looking at the options with the 'tractstats2table' utility. Jim "The

Re: [Freesurfer] -qcache in recon-all commnd

On Behalf Of Alexopoulos, Dimitrios Sent: Friday, May 25, 2018 12:47 PM To: Freesurfer support list Subject: Re: [Freesurfer] -qcache in recon-all commnd External Email - Use Caution Any further comments on the correct command to run after making manual edits. Specifically, should the '-hippocampal

Re: [Freesurfer] -qcache in recon-all commnd

email in error, please immediately notify the sender via telephone or return email." -Original Message- From: freesurfer-boun...@nmr.mgh.harvard.edu [mailto:freesurfer-boun...@nmr.mgh.harvard.edu] On Behalf Of Alexopoulos, Dimitrios Sent: Wednesday, May 23, 2018 10:38 AM To: Freesurf

Re: [Freesurfer] -qcache in recon-all commnd

it. Maybe Eugenio can weigh in On 05/22/2018 12:11 PM, Alexopoulos, Dimitrios wrote: > External Email - Use Caution > > Thanks Doug. > > Sorry for the multiple posts. I forgot to mention that the original recon-all > run included the '-hippocampal-subfields-T1' f

Re: [Freesurfer] -qcache in recon-all commnd

s to speed things up. On 05/21/2018 04:48 PM, Alexopoulos, Dimitrios wrote: > External Email - Use Caution > > We have not re-run anything yet. The data was originally generated using' > recon-all -s -all -hires -qcache'. > > We have since made manual edits to the wm,

Re: [Freesurfer] -qcache in recon-all commnd

8 04:36 PM, Alexopoulos, Dimitrios wrote: > External Email - Use Caution > > Ok. So no my '-all' flag? > I just want to make sure as we're re-running a 100+ edited subjects and I > had read elsewhere that the '-all' flag is required. > > Jim > > > "The materi

Re: [Freesurfer] -qcache in recon-all commnd

all commnd You don't even need to include -hires (though I don't think it hurts anything) On 05/21/2018 04:25 PM, Alexopoulos, Dimitrios wrote: > External Email - Use Caution > > OK, so I only need to run a single command to incorporate the all edits: > recon-all -s subj

Re: [Freesurfer] -qcache in recon-all commnd

en you run -qcache, do not include -all On 05/21/2018 04:02 PM, Alexopoulos, Dimitrios wrote: > External Email - Use Caution > > Just want to confirm which command to issue to rerun 6.0 incorporating manual > edits to the wm.mgz, brainmask.mgz andadding control

Re: [Freesurfer] -qcache in recon-all commnd

Freesurfer] -qcache in recon-all commnd Yes, I think so On 05/07/2018 10:35 PM, Alexopoulos, Dimitrios wrote: > External Email - Use Caution > > I ran 'recon-all -all -hires -qcache' on several datasets. I made numerous > edits of the brainmansk.mgz (for dura removal) an

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