Re: [Freesurfer] template label map

2013-04-03 Thread Bruce Fischl
Hi Johnson what do you mean? There are a number of different atlases we use, but none of them are strictly speaking a template, except the Talairach one I guess. cheers Bruce On Wed, 3 Apr 2013, Johnson wrote: Dear FS Can you please tell me what is the default template file used in the

Re: [Freesurfer] Bad Talairach Registration

2013-04-03 Thread Bruce Fischl
Ae you trying to put a diffusion scan through recon-all? That won't work, it needs to be T1 weighted Bruce On Apr 3, 2013, at 10:23 PM, Cherise R. Chin Fatt cherise.chinf...@utdallas.edu wrote: Hello: I have been trying to use FreeSurfer on an aging population and running into

Re: [Freesurfer] Bad Talairach Registration

2013-04-03 Thread Bruce Fischl
Do you know why it has multiple frames? What kind of image is it? On Apr 3, 2013, at 10:51 PM, Cherise R. Chin Fatt cherise.chinf...@utdallas.edu wrote: Hello Bruce: I am using a T1-weighted image. On Wed, Apr 3, 2013 at 9:44 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote

Re: [Freesurfer] Fw: Making cuts using tksurfer

2013-04-04 Thread Bruce Fischl
- From: Anupa AV av.an...@yahoo.com To: Bruce Fischl fis...@nmr.mgh.harvard.edu Sent: Wednesday, April 3, 2013 11:57 AM Subject: Re: [Freesurfer] Making cuts using tksurfer Dear Sir, As you recommended, I have made a cut using plane option. Kindly see the attachment. My research interst is to make

Re: [Freesurfer] Doubt in the no. of dicom images

2013-04-04 Thread Bruce Fischl
this is for the same acquisition? You should definitely try to avoid that as it will change the SNR. Bruce On Wed, 3 Apr 2013, Anupa AV wrote: Dear All, I use Philips Achieva 3T scanner for the MRI study. When I open the Dicom folder, (say for MPR ) the no. of items I can see is 222

Re: [Freesurfer] mri_robust_register to obtain jacobian

2013-04-04 Thread Bruce Fischl
Hi Jay for the rigid case the jacobian is always the same. cheers Bruce On Thu, 4 Apr 2013, Jayachandra Raghava wrote: Hello All, I am trying to use mri_robust_register to compute the symmetric rigid registration for inverse consistency. Is there a way to output the inverse consistent

Re: [Freesurfer] Intensity Normalization

2013-04-05 Thread Bruce Fischl
Hi Dan if the surfs look good you are all set. Does it go from left to right or right to left? Rightmost temporal lobes look the darkest to me. I would have thought you would still need some control points, but if not that's great Bruce On Fri, 5 Apr 2013, Dan LaFreniere wrote: Dear

Re: [Freesurfer] bblabels??

2013-04-06 Thread Bruce Fischl
mri_label2label maps them in whatever direction you specify. Someone else will have to answer the bblabels question as I don't know what it is cheers Bruce On Fri, 5 Apr 2013, Anupa AV wrote: Hello experts, I'm in a process to make coronal cuts using tksurfer Please help me with the

Re: [Freesurfer] makelabels error

2013-04-06 Thread Bruce Fischl
Hi Jeff have you looked at the labels? That error frequently means something is wrong in the coordinate transforms. Look at the label in the volume and see if it is where you think it should be. cheers Bruce On Sat, 6 Apr 2013, jwa...@nmr.mgh.harvard.edu wrote: Hello, I am trying to adapt

Re: [Freesurfer] Making mid-gray surfaces without mris_expand?

2013-04-06 Thread Bruce Fischl
Hi Keith the average white/pial surface doesn't have any topological or smoothness constraints, which is why we don't really use it. Yes, mris_expand is slow, but that's precisely because it prohibits self-intersection. The good nes is that compared to the rest of the recon stream it doesn't

Re: [Freesurfer] fsaverage mappings

2013-04-06 Thread Bruce Fischl
Hi Satra the first 12 vertices will be from the 0th order icosahedron, the next 30 from the 2nd order, etc Bruce On Sat, 6 Apr 2013, Satrajit Ghosh wrote: hi folks, are there predefined mappings between the fsaverage surfaces? for example, i have an array of numbers for all the

Re: [Freesurfer] Intensity Normalization

2013-04-06 Thread Bruce Fischl
at 11:09 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Dan if the surfs look good you are all set. Does it go from left to right or right to left? Rightmost temporal lobes look the darkest to me. I would have thought you would still need some control

Re: [Freesurfer] Making mid-gray surfaces without mris_expand?

2013-04-06 Thread Bruce Fischl
in the average? -Keith On Sat, Apr 6, 2013 at 7:59 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Keith the average white/pial surface doesn't have any topological or smoothness constraints, which is why we don't really use it. Yes, mris_expand is slow, but that's

Re: [Freesurfer] Confused with Coordinate System in FS

2013-04-07 Thread Bruce Fischl
there is pretty extensive documentation on the (always confusing) coordinate systems we use - we do *not* resample into tal coords - all calculations are done in subject native space, after resampling to 256^3, 1mm iso (which we call conforming for no very good reason) - The talairach.xfm

Re: [Freesurfer] Problem at tksurfer

2013-04-08 Thread Bruce Fischl
Hi Benjamin what format are the images in? They don't have an extension. thanks Bruce On Mon, 8 Apr 2013, Roschinski, Benjamin wrote: Von: Roschinski, Benjamin Gesendet: Donnerstag, 31. Januar 2013 13:37 An: freesurfer-ow...@nmr.mgh.harvard.edu

Re: [Freesurfer] Problem at tksurfer

2013-04-09 Thread Bruce Fischl
Hi Benjamin what version of FS are you using? I'm surprised by the little spot of none in the cuneus, not sure what caused that. Does the aseg look okay? It does look like insula is extending too far medially. What are you intending to do with these data? These relatively minor problems may

Re: [Freesurfer] Fw: Making cuts using tksurfer

2013-04-09 Thread Bruce Fischl
-volumes (e.g., medial and lateral)? Thanks, Jeff - Forwarded Message - From: Anupa AV av.an...@yahoo.com To: Bruce Fischl fis...@nmr.mgh.harvard.edu Sent: Friday, April 5, 2013 11:24 AM Subject: Re: [Freesurfer] Fw: Making cuts using tksurfer Dear Sir, Kindly see the attachment. I

Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0

2013-04-10 Thread Bruce Fischl
We are investigating it. I did fix one thing that you can try if you want - give us your hardware/software info and we will send you a new version of mris_make_surfaces Bruce P.s. you can also upload and we will take a look On Apr 10, 2013, at 6:11 AM, Yang, Daniel yung-jui.y...@yale.edu

Re: [Freesurfer] Very different results between 5.1.0 and 5.2.0

2013-04-10 Thread Bruce Fischl
Hi PPJ That's exactly what we are doing. Good to hear its stable for you Bruce On Apr 10, 2013, at 8:38 AM, Pedro Paulo de Magalhães Oliveira Juniorp...@netfilter.com.br wrote: I have processed more that 600 brains with both versions in the last weeks and the only difference I'm seeing

Re: [Freesurfer] Finding adjacent vertices/labels

2013-04-10 Thread Bruce Fischl
Hi Chris the easiest way would be to load the surfaces and parcellation in in matlab and look for adjacency that way Bruce On Wed, 10 Apr 2013, Chris McNorgan wrote: Hello Freesurfers, I was wondering if there is information embedded in the annotation/label files that could be used to

Re: [Freesurfer] mgz to dicom

2013-04-11 Thread Bruce Fischl
Sorry, we don't write dicom usually, just read it Bruce On Apr 11, 2013, at 8:27 AM, Varghese Chikku chik...@tcd.ie wrote: Hi All, Is there any tool,which can convert mgz files to Dicom? In Thanks chikku ___ Freesurfer mailing list

Re: [Freesurfer] Autoreg-sess and mri_surf2vol

2013-04-11 Thread Bruce Fischl
Hi Lucille what do you mean by converting a surface to the volume? What do you want to do with it? What volume would you like to convert it to? cheers Bruce On Thu, 11 Apr 2013, Lucille Deroche wrote: Hi,  My name is Lucille and I'm really new  with Freesurfer : My questions are very

Re: [Freesurfer] Autoreg-sess and mri_surf2vol

2013-04-11 Thread Bruce Fischl
surfaces in volume to be able to calculate the dice score between the two. Cheers Lucille *De :* Bruce Fischl fis...@nmr.mgh.harvard.edu *À :* Lucille Deroche lucilledero...@yahoo.fr *Cc :* freesurfer@nmr.mgh.harvard.edu

[Freesurfer] announcement for MGH email list (fwd)

2013-04-12 Thread Bruce Fischl
FYI -- Forwarded message -- Date: Fri, 12 Apr 2013 00:27:38 +0200 From: Jorge Jovicich jorge.jovic...@unitn.it To: Bruce Fischl fis...@nmr.mgh.harvard.edu Subject: announcement for MGH email list Ciao Bruce, would you mind forwarding for me the postdoc position announcement below

Re: [Freesurfer] Autoreg-sess and mri_surf2vol

2013-04-12 Thread Bruce Fischl
will compare the results and I'll give you a feedback. Cheers Lucille *De :* Bruce Fischl fis...@nmr.mgh.harvard.edu *À :* Michael Harms mha...@conte.wustl.edu *Cc :* Lucille Deroche lucilledero...@yahoo.fr; freesurfer

Re: [Freesurfer] unit of corpus callosum segmentation

2013-04-12 Thread Bruce Fischl
Hi Marie, 400 or 900 what? Not mm. How are you calculating thickness? I think in Diana's paper it was the radius of the inscribed circle on the medial axis, wasn't it? Bruce On Apr 12, 2013, at 10:44 PM, Marie Schaer marie.sch...@unige.ch wrote: Hi all, I have a quick question related to

Re: [Freesurfer] unit of corpus callosum segmentation

2013-04-13 Thread Bruce Fischl
was measured as the thickness / distance from the medial axis of the CC to the superior and inferior boundaries, but I may have wrongly understood. Thanks for the clarification, Marie On Apr 12, 2013, at 8:07 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Marie, 400

[Freesurfer] 5.2 pial surfaces

2013-04-13 Thread Bruce Fischl
Hi All we've tracked down the problem with 5.2 pial surfaces that affects some types of acquisitions. We will be testing the fixed version this week and hope to release a corrected mris_make_surfaces in the near future. You should just be able to rerun autorecon2 I believe to update your

Re: [Freesurfer] unit of corpus callosum segmentation

2013-04-14 Thread Bruce Fischl
assume that I can divide these values by 5 and present them as area of the CC on the midline section, right? Have a nice week-end, Marie On Apr 13, 2013, at 5:18 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Marie It is mm^3 of I believe a 5 mm thick cc. We don't measure

Re: [Freesurfer] creating new curv/thick/area files using tweaked white/pial

2013-04-15 Thread Bruce Fischl
Hi Fred mris_thickness will make thickness. Not sure we have anything to make area. I guess you could try setting -n 0 in mris_make_surfaces to it runs for 0 iterations. Or we can put something together to create area - it should be trivial cheers Bruce On Mon, 15 Apr 2013, Fred Dick wrote:

Re: [Freesurfer] pial surface with FLAIR

2013-04-15 Thread Bruce Fischl
Hi Veronica, we haven't seen that before. Can you upload your subject including the FLAIR and we'll take a look? thanks Bruce On Mon, 15 Apr 2013, Popescu, Veronica wrote: Dear all, I have already run the FreeSurfer 5.2 -all, and I would like to improve the pial surface recongition using

Re: [Freesurfer] pial surface with FLAIR

2013-04-16 Thread Bruce Fischl
steps: recon-all -autorecon3 -s $SUBJECT -FLAIRpial It has worked for me. (And worked very well! No edits necessary for the pial surface!) From: freesurfer-boun...@nmr.mgh.harvard.edu [freesurfer-boun...@nmr.mgh.harvard.edu] on behalf of Bruce

Re: [Freesurfer] pial surface with FLAIR

2013-04-16 Thread Bruce Fischl
, Veronica -Original Message- From: Watson, Christopher [mailto:christopher.wat...@childrens.harvard.edu] Sent: Tuesday, 16 April, 2013 07:15 To: Bruce Fischl; Popescu, Veronica Cc: 'freesurfer@nmr.mgh.harvard.edu' Subject: RE: [Freesurfer] pial surface with FLAIR Hi Veronica, Did you

Re: [Freesurfer] pial surface with FLAIR

2013-04-16 Thread Bruce Fischl
, Veronica -Original Message- From: Bruce Fischl [mailto:fis...@nmr.mgh.harvard.edu] Sent: Tuesday, 16 April, 2013 15:02 To: Popescu, Veronica Cc: 'Watson, Christopher'; 'freesurfer@nmr.mgh.harvard.edu' Subject: RE: [Freesurfer] pial surface with FLAIR Hi Veronica what recon-all command

Re: [Freesurfer] 5.2 pial surfaces

2013-04-16 Thread Bruce Fischl
glad to hear it Bruce On Tue, 16 Apr 2013, Yang, Daniel wrote: Thanks so much for the improvement! I ran the new mris_make_surfaces and the pial surfaces look much better in FS 5.2! Here is the comparison slice if you're interested.

Re: [Freesurfer] defect 0

2013-04-17 Thread Bruce Fischl
Hi Chikku a 30,000 vertex defect means something is dramatically wrong - that's about 1/4 of the whole cortex. Check your filled.mgz or lh.orig.nofix and see if the skull is attached or the cerebellum or something. The computational complexity of the topology fixing is quadratic in the

Re: [Freesurfer] Template from scratch

2013-04-17 Thread Bruce Fischl
Hi Sophie, if you want the template to represent corresponding points across your subjects you need to use sphere.reg cheers Bruce On Wed, 17 Apr 2013, Sophie Maingault wrote: Hi Experts, I'm creating a template from scratch. When I run mris_make_template is it enough to run 

Re: [Freesurfer] Template from scratch

2013-04-17 Thread Bruce Fischl
across subjects ? Sophie Le 17/04/13 15:42, « Bruce Fischl » fis...@nmr.mgh.harvard.edu a écrit : Hi Sophie, if you want the template to represent corresponding points across your subjects you need to use sphere.reg cheers Bruce On Wed, 17 Apr 2013, Sophie Maingault wrote: Hi Experts, I'm

Re: [Freesurfer] Crash reports on several situations.

2013-04-17 Thread Bruce Fischl
Hi Nate how much memory do you have in the machine? Bruce On Wed, 17 Apr 2013, Nate Lee wrote: Hello everyone, I'm using Freesurfer from Texas Medical Center. I'm using an iMac, and am experiencing regular crashes during these several occasions: 1. Opening more than two volumes at once 2.

Re: [Freesurfer] Crash reports on several situations.

2013-04-17 Thread Bruce Fischl
Hi Nate how much RAM is there, not disk space. cheers Bruce On Wed, 17 Apr 2013, Nate Lee wrote: Hello Bruce, The iMac has 500GB capacity, and 425GB is not in use. Best regards, Nate  On Wed, Apr 17, 2013 at 12:06 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Nate

Re: [Freesurfer] error while performing recon-all for multiple datasets

2013-04-18 Thread Bruce Fischl
Hi Anupa you need to specify each input volume with -i if there are more than one. In your example you would need an inner loop of the form set inputs = () foreach vol (SZ*.nii) set input = ($inputs -i $vol) end recon-all $inputs ... cheers Bruce On Wed, 17 Apr 2013, Anupa AV wrote:

Re: [Freesurfer] autorecon2-cp error

2013-04-18 Thread Bruce Fischl
Hi Claudia that defect is bigger than more cortical surfaces so something is dramatically wrong. Did you check any of the outputs (wm.mgz, filled.mgz, lh.orig, etc...)? cheers Bruce On Thu, 18 Apr 2013, Claudia Dacquino wrote: Hi freesurfer,  my autorecon2-cp after ctrl pts edits exited

Re: [Freesurfer] Merging the labels to T1 image

2013-04-20 Thread Bruce Fischl
that's possible with FS? From: Bruce Fischl fis...@nmr.mgh.harvard.edu To: Anupa AV av.an...@yahoo.com Cc: Freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Saturday, April 20, 2013 7:25 PM Subject: Re: [Freesurfer] Merging the labels to T1 image Hi Anupa I'm not sure what you mean

Re: [Freesurfer] Merging the labels to T1 image

2013-04-22 Thread Bruce Fischl
. __ From: Shantanu Ghosh shant...@nmr.mgh.harvard.edu To: Anupa AV av.an...@yahoo.com Cc: Bruce Fischl fis...@nmr.mgh.harvard.edu; Freesurfer freesurfer@nmr.mgh.harvard.edu Sent: Sunday, April 21, 2013 9:44 AM Subject: Re: [Freesurfer] Merging the labels to T1 image Hi Anupa- you can

Re: [Freesurfer] Where does a sulcus end and a gyrus begin in FreeSurfer?

2013-04-22 Thread Bruce Fischl
Hi Daniel we have had various neuroanatomists make that decision, but the typical measure used is the average convexity or sulc (stored in ?h.sulc). Where it crosses 0 is where the changeover is usually deemed to be cheers Bruce On Mon, 22 Apr 2013, Yang, Daniel wrote: Dear FreeSurfer

Re: [Freesurfer] surfer.nmr.mgh.harvard.edu down?

2013-04-24 Thread Bruce Fischl
Hi Graham yes, we have been the target of a denial-of-service attack and have taken it offline for external users for a bit Bruce On Wed, 24 Apr 2013, Graham Wideman wrote: Hi MGH-ers, From where I sit (San Diego), http://surfer.nmr.mgh.harvard.edu/ seems to have been non-responsive at

Re: [Freesurfer] Correcting bad segmentation/WM surfacing

2013-04-25 Thread Bruce Fischl
Hi Jonathon that's pretty bad. Did the skull stripping fail? If you upload the subject I'll take a look Bruce On Thu, 25 Apr 2013, Jonathan Holt wrote: See attached image for reference. Large area has been incorrectly segmented as WM, also WM surface has completely been skipped over.

Re: [Freesurfer] mri_ms_fitparms_questions

2013-04-25 Thread Bruce Fischl
Hi Dan how do you do the B1 correction? And why would we need to know the field strength? The T1 is certainly a function of the field strength, but we will just find the T1 for whatever strength field the input data was acquired with. And yes, we search in 5ms increments. You could certainly

Re: [Freesurfer] adding grey matter

2013-04-29 Thread Bruce Fischl
Hi Claudia it really depends on the individual case and what's causing the exclusion. Does the wm.mgz look accurate? If so, you may have a topological defect that is being fixed incorrectly. Usually we focus on fixing the white boundary and that will also correct the pial. You can set the

Re: [Freesurfer] FLASH params for mri_em_register

2013-04-29 Thread Bruce Fischl
Hi Fred we don't have much experience with this. Which synthesis are you using? You might need to use a different one for the talairaching to more closely match the atlas (maybe a TR=20,TE=2.5,flip=20-30 one) On Mon, 29 Apr 2013, Fred Dick wrote: Dear all I'm having difficulties getting

Re: [Freesurfer] adding grey matter

2013-04-29 Thread Bruce Fischl
see that there are control points added (green cosses), but they seem  not to be processed by the autorecon2-cp autorecon3. Thanks Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Claudia can you describe the problems? And cc the list so that others can help

Re: [Freesurfer] FLASH params for mri_em_register

2013-04-29 Thread Bruce Fischl
- but possibly irrelevant as also have the -w flag on. I originally thought this was from a bad brainmask, but then generated a good one and same thing happening. On 29 Apr 2013, at 14:27, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Fred we don't have much experience with this. Which

Re: [Freesurfer] adding grey matter

2013-04-29 Thread Bruce Fischl
then it's not rerunning the -cp. And is it really wm if it's that dark? On Mon, 29 Apr 2013, Claudia Dacquino wrote: Bruce,no the intensity is lesser then 110 at those voxels, it's like 60-70. Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu is the intensity at those voxels

Re: [Freesurfer] adding grey matter

2013-04-29 Thread Bruce Fischl
visually is the only way. Do you think it is white matter? On Mon, 29 Apr 2013, Claudia Dacquino wrote: Yes it's my doubt too, but how can I check this? 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu then it's not rerunning the -cp. And is it really wm if it's that dark

Re: [Freesurfer] adding grey matter

2013-04-29 Thread Bruce Fischl
, but I'm quite sure that there is grey matter excluded by pial bounaries as well, how can I add that? 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu visually is the only way. Do you think it is white matter? On Mon, 29 Apr 2013, Claudia Dacquino wrote: Yes it's my

Re: [Freesurfer] adding grey matter

2013-04-29 Thread Bruce Fischl
matter, but looking with more attention at wm.mgz I did realize that they could me no WM, as you seggested me, because they are too dark.  I'm new and I'm learning by trial and error. Cheers, Claudia 2013/4/29 Bruce Fischl fis...@nmr.mgh.harvard.edu Hi Claudia now I'm confused. Did

Re: [Freesurfer] FLASH params for mri_em_register

2013-04-30 Thread Bruce Fischl
2013, at 15:05, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: yes, the -w will create an optimal weighting to maximize gray/white contrast. The image it generates won't in general be physically realizable in an real MR acquisition. Not surprising that the tal stuff fails On Mon, 29 Apr 2013

Re: [Freesurfer] FLASH params for mri_em_register

2013-04-30 Thread Bruce Fischl
Hi Fred, I'll have to defer to Doug on this Bruce On Tue, 30 Apr 2013, Fred Dick wrote: Hi Bruce On 30 Apr 2013, at 13:36, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Fred I know it's a silly question but are you sure that file exists and is readable by you? The fact that it's

Re: [Freesurfer] setting up FS

2013-05-01 Thread Bruce Fischl
Hi Asha, from the screen shot it looks like FS is installed properly. Have you tried running it? You could try: tksurfer fsaverage lh inflated -curv cheers Bruce On Wed, 1 May 2013, Ash Rafea wrote: Hi there, I am totally a begginer in the Neurodebian world so please be patient :( I

Re: [Freesurfer] Visualize a fixed number of voxels using Tksurfer

2013-05-01 Thread Bruce Fischl
Hi Martin I guess you could do this using the histogram in tksurfer (left and right clicking in it will set the min and max thresholds). Or it would be pretty easy in matlab. cheers Bruce On Wed, 1 May 2013, Martin Bleichner wrote: Hi all,  is there a way to visualize a fixed number of

Re: [Freesurfer] How to flip L/R image in the freeview?

2013-05-01 Thread Bruce Fischl
Hi Glen have you done the cross-hemisphere registration? If so, you can do this with mri_surf2surf, although the syntax is a bit tricky. Doug would know the details, but he's probably not going to be able to answer questions until tomorrow cheers Bruce On Wed, 1 May 2013, Glen Lee wrote:

Re: [Freesurfer] error in longitudinal processing dimension mismatch

2013-05-01 Thread Bruce Fischl
Keith On Wed, May 1, 2013 at 12:43 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Keith can you cc the list so that others can answer? Like Martin! thanks Bruce On Wed, 1 May 2013, Qi Wu wrote: Hi Bruce, Thank you so much for your quick reply

Re: [Freesurfer] (no subject)

2013-05-01 Thread Bruce Fischl
Hi Ashley yes, a bunch of times. The dura can cause some problems, but mostly they run ok Bruce On Wed, 1 May 2013, Ashley Hannah wrote: Has anyone ever ran a post contrast sequence in FreeSurfer? Thanks,  Ashley -- ___ Freesurfer mailing list

Re: [Freesurfer] Using the muscle ROI in the FreeSurferColorLUT

2013-05-01 Thread Bruce Fischl
Hi Jeff our standard segmentation doesn't include muscle. We did have some prototypes that labeled all cranial muscles but they are not much more than prototypes Bruce On Wed, 1 May 2013, jwa...@nmr.mgh.harvard.edu wrote: Hello Freesurfers, I would like to use the muscle ROI in the LUT

Re: [Freesurfer] tip and tricks with patient with one big ventricle...

2013-05-02 Thread Bruce Fischl
what version are you running? The newer ones are *much* better at this Bruce On Thu, 2 May 2013, Gonzalo Rojas Costa wrote: Hi: I has the MPRAGE of a patient with one big ventricle, and the other has normal shape and size... Any tip and tricks to process it ?... Because freesurfer fails

Re: [Freesurfer] tip and tricks with patient with one big ventricle...

2013-05-02 Thread Bruce Fischl
, May 2, 2013 at 1:31 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: what version are you running? The newer ones are *much* better at this Bruce On Thu, 2 May 2013, Gonzalo Rojas Costa wrote: Hi:  I has the MPRAGE of a patient

[Freesurfer] version 5.3 coming out soon

2013-05-02 Thread Bruce Fischl
Hi All, We have recently uncovered problems with version 5.2. Based on these problems, we are recommending that people stop using 5.2, mainly in regards to usage of the surface data. A new version, 5.3, will be released within two weeks, and a beta version for each platform will be available

Re: [Freesurfer] Flattening a specific surface parcellation or a group of spatially adjacent parcellations

2013-05-02 Thread Bruce Fischl
Hi Bilal I think I wrote something called label2patch or label2flat for this propose. Let me know if you can't find it. You will still need to run mris_flatten on each patch Bruce On May 2, 2013, at 1:54 PM, Bilal Ahmed shibl...@gmail.com wrote: Hi, I was wondering if there is a simple

Re: [Freesurfer] Flattening a specific surface parcellation or a group of spatially adjacent parcellations

2013-05-02 Thread Bruce Fischl
for something like that. doug On 5/2/13 9:31 PM, Bruce Fischl wrote: Hi Bilal I think I wrote something called label2patch or label2flat for this propose. Let me know if you can't find it. You will still need to run mris_flatten on each patch Bruce On May 2, 2013, at 1:54 PM, Bilal

Re: [Freesurfer] tip and tricks with patient with one big ventricle...

2013-05-03 Thread Bruce Fischl
On Thu, May 2, 2013 at 9:29 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Gonzalo Try it with 5.3, or upload and I can r. It for you Bruce On May 2, 2013, at 2:16 PM, Gonzalo Rojas Costa gonzalo.rojas.co...@gmail.com wrote: Hi Bruce: I tested 4.5 and 5.1 versions... with the first I

Re: [Freesurfer] Question

2013-05-03 Thread Bruce Fischl
Hi Beth it depends on what kinds of artifacts it causes. I would think it would be ok, but don't have any experience. Bruce On Fri, 3 May 2013, Jerskey, Beth wrote: What effect, if any, would the implantation of a Vagus Nerve Stimulator have on registration? Thank you, Beth

Re: [Freesurfer] epi correction of fmri data

2013-05-03 Thread Bruce Fischl
Hi Corinna yes, we use the FSL tools for B0 correction. cheers Bruce On Fri, 3 May 2013, Corinna Bauer wrote: Is there a way to correct fmri data for epi distortions in freesurfer? Or does the data need to be first fun through FSL's B0 unwarping? Corinna

Re: [Freesurfer] tip and tricks with patient with one big ventricle...

2013-05-03 Thread Bruce Fischl
ok, I think Nick posted a link of where the beta will be (or if not, he will) Bruce On Fri, 3 May 2013, Gonzalo Rojas Costa wrote: Hi Bruce: Ok... I am interested in the 5.3 beta version... Sincerely, Gonzalo Rojas Costa On Fri, May 3, 2013 at 8:41 AM, Bruce Fischl fis

Re: [Freesurfer] Using mri_cor2label

2013-05-03 Thread Bruce Fischl
Hi Jeff Don't you want the aparc+aseg not the aseg? Bruce On May 3, 2013, at 10:37 PM, jwa...@nmr.mgh.harvard.edu wrote: Thanks Doug, The command line I am running is: mri_cor2label --c /cluster/ablood/1/${experimental_directory}/${recons_directory}/${identifier}_recon/mri/aseg.mgz

Re: [Freesurfer] version 5.3 coming out soon

2013-05-04 Thread Bruce Fischl
schrieb Bruce Fischl fis...@nmr.mgh.harvard.edu: Hi All, We have recently uncovered problems with version 5.2. Based on these problems, we are recommending that people stop using 5.2, mainly in regards to usage of the surface data.  A new version, 5.3, will be released within two weeks

Re: [Freesurfer] Pial surface errors

2013-05-06 Thread Bruce Fischl
Hi Valeria what version are you running? It's hard to tell from a single slice, but what is the white-matter appearing stuff that is outside the white matter surface? I think that is what's messing stuff up. If you want to upload the data subject one of us will take a look (that is, upload the

Re: [Freesurfer] repeat: trouble loading nifti files

2013-05-07 Thread Bruce Fischl
Hi Akshay is you send us that file we'll take a look. cheers Bruce On Tue, 7 May 2013, Akshay wrote: Hi All, I am re-posting this question since there was no response to my previous attempt. I have a problem conforming certain nifti files, the following is the log when i try to convert

Re: [Freesurfer] Fwd: Re: repeat: trouble loading nifti files

2013-05-07 Thread Bruce Fischl
Fischl wrote: can you send me the full mri_convert command line that is run? On Tue, 7 May 2013, Akshay wrote: Hi Bruce Please find the file attached Best, Akshay On 5/7/13 2:40 PM, Bruce Fischl wrote: Hi Akshay is you send us that file we'll take a look. cheers Bruce On Tue, 7 May

Re: [Freesurfer] using T2* weighted scans to assist with dura stripping in a GE scanner?

2013-05-07 Thread Bruce Fischl
Hi Katie I'm really not sure. These days I would recommend a highres (e.g. 1mm isotropic) FLAIR if you can get one, or T2 if not. The T2* can help, but it's pretty noisy in brain. cheers Bruce On Tue, 7 May 2013, Katie Surrence wrote: Dear Freesurfer gurus, At the course, André van der

Re: [Freesurfer] using T2* weighted scans to assist with dura stripping in a GE scanner?

2013-05-07 Thread Bruce Fischl
Facility NIMH/NIH/DHHS souheil.in...@nih.govmailto:souheil.in...@nih.gov On May 7, 2013, at 2:24 PM, Bruce Fischl fis...@nmr.mgh.harvard.edumailto:fis...@nmr.mgh.harvard.edu wrote: Hi Katie I'm really not sure. These days I would recommend a highres (e.g. 1mm isotropic) FLAIR if you can get one

Re: [Freesurfer] using T2* weighted scans to assist with dura stripping in a GE scanner?

2013-05-07 Thread Bruce Fischl
actually Matt Glasser points out that a brief description is in his paper that is coming out soon, and there is also some description in Andre's multi-echo mprage paper Bruce On Tue, 7 May 2013, Inati, Souheil (NIH/NIMH) [E] wrote: thanks :-) On May 7, 2013, at 3:28 PM, Bruce Fischl fis

Re: [Freesurfer] Issues in version 5.2

2013-05-08 Thread Bruce Fischl
Hi Stefano it will have some effect due to the changes in the white matter placement, but probably not a big one (and it's hard to say whether the changes are good or bad). The results should certainly be reliable cheers Bruce On Wed, 8 May 2013, std...@virgilio.it wrote: I apologize for

Re: [Freesurfer] (no subject)

2013-05-08 Thread Bruce Fischl
Hi Shani what kind of segmentation? In general yes, but you'll need to mess with the recon-all script cheers Bruce On Wed, 8 May 2013, Shani Ben Amitay wrote: Hello Freesurfer I would like to extract the stream for surface-based analysis on the output of an in-house segmentation

Re: [Freesurfer] mri_convert Segmentation fault

2013-05-08 Thread Bruce Fischl
Hi Oscar if you send us the file and the command line we'll see if we can replicate and fix. cheers Bruce On Wed, 8 May 2013, Oscar Esteban wrote: Dear all, I am experiencing segfaults when trying to convert from nifti to mgz. Ubuntu 13.04 Freesurfer 5.1, 5.2 and 5.3-BETA. I tried to

Re: [Freesurfer] (no subject)

2013-05-08 Thread Bruce Fischl
! Shani On Wed, May 8, 2013 at 3:46 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Shani what kind of segmentation? In general yes, but you'll need to mess with the recon-all script cheers Bruce On Wed, 8 May 2013, Shani Ben Amitay wrote

Re: [Freesurfer] (no subject)

2013-05-08 Thread Bruce Fischl
? On Wed, May 8, 2013 at 4:24 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: oh, that's going to be tough. I guess you could extract the WM and use it to create our wm.mgz and go from there On Wed, 8 May 2013, Shani Ben Amitay wrote: Segmentation into white matter

Re: [Freesurfer] Normalization Errors?

2013-05-08 Thread Bruce Fischl
Hi Gonzalo it's hard to tell from just that image. What does it look like before normalization (e.g. the nu.mgz or orig.mgz)? Is there gray/white contrast there? cheers Bruce On Wed, 8 May 2013, Gonzalo Iribarne wrote: Hello Freesurfers, There are some areas of grey and white matter that

Re: [Freesurfer] Working with MEMPRAGE

2013-05-09 Thread Bruce Fischl
Hi Jon yes, the subject and hemi need to be defined (they are required parameters) Bruce On Wed, 8 May 2013, Jonathan Holt wrote: Hi all, combed through the mail archives to figure out how to work with multi echo mprage, found what I need but I wanted to confirm which of these two commands

Re: [Freesurfer] Working with MEMPRAGE

2013-05-09 Thread Bruce Fischl
detecting dura using 0 echos from memprage_echo%d.mgz be worrisome? I've got 4 different echos, all mgzs in the directory. I have a feeling I'm doing this incorrectly. jon On May 9, 2013, at 8:50 AM, Bruce Fischl wrote: Hi Jon yes, the subject and hemi need to be defined

Re: [Freesurfer] Working with MEMPRAGE

2013-05-09 Thread Bruce Fischl
%d.mgz Should I execute the command in the same directory as the mgz's? Should they be set up or placed in a specific directory? I also, as with recon-all, exported the proper subject directory beforehand. On May 9, 2013, at 10:37 AM, Bruce Fischl wrote: can you send me the full command

Re: [Freesurfer] Working with MEMPRAGE

2013-05-09 Thread Bruce Fischl
) and nothing else. Also the exact error has it looking in /example/directory/subjects/memprage_echo%d.mgz/mri/filled.mgz as opposed to /example/directory/subjects/subjid/mri/filled.mgz I can rename subject directory if need be. On May 9, 2013, at 10:54 AM, Bruce Fischl wrote: is your

Re: [Freesurfer] Working with MEMPRAGE

2013-05-09 Thread Bruce Fischl
, at 11:04 AM, Bruce Fischl wrote: Did you run recon-all? It will create filled.mgz in the subject/mri dir On May 9, 2013, at 11:00 AM, Jonathan Holt whats...@umich.edu wrote: That was my suspicion, I've got them in the wrong folder. None of them are 'filled.mgz' though, I've only got 4

Re: [Freesurfer] Working with MEMPRAGE

2013-05-09 Thread Bruce Fischl
gets put into one mgz file, and the RMS gets put into a separate mgz file. Thanks, -Kayle On May 9, 2013, at 12:00 PM, freesurfer-requ...@nmr.mgh.harvard.edu wrote: Message: 35 Date: Thu, 9 May 2013 10:44:23 -0400 (EDT) From: Bruce Fischl fis...@nmr.mgh.harvard.edu Subject: Re: [Freesurfer

Re: [Freesurfer] Working with MEMPRAGE

2013-05-10 Thread Bruce Fischl
only the RMS in recon-all (ie , that is the only volume that goes into mri/orig doug On 5/9/13 6:48 PM, Bruce Fischl wrote: Hi Kayle you would run recon-all on the RMS, then run the dura stuff posthoc. cheers Bruce On Thu, 9 May 2013, Kayle Sawyer wrote: Hi all, Can the MEMPRAGE

Re: [Freesurfer] Working with MEMPRAGE

2013-05-10 Thread Bruce Fischl
is in s_MEMPRAGE/mri/orig.  On Fri, May 10, 2013 at 12:33 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: can you send details about the steps you carried out including full command lines? On Fri, 10 May 2013, Jonathan Holt wrote: I've gotten as far as running

Re: [Freesurfer] Working with MEMPRAGE

2013-05-10 Thread Bruce Fischl
on the RMS'd nifti, then recon-all on that. I don't understand how I can go from 1 RMS'd mgz back to 4 separate echos? jon On May 10, 2013, at 12:41 PM, Bruce Fischl wrote: did you run recon-all -all all the way through? you should name your echoes something different like echo1.mgz, echo2.mgz

Re: [Freesurfer] Working with MEMPRAGE

2013-05-10 Thread Bruce Fischl
, Bruce Fischl wrote: did you run recon-all -all all the way through? you should name your echoes something different like echo1.mgz, echo2.mgz... then specify -dura echo%d.mgz 4 cheers Bruce On Fri, 10 May 2013, Jonathan Holt wrote: $ export SUBJECTS_DIR=/net/data4/ALSSCI/FreeSurfer201211

Re: [Freesurfer] using T2* weighted scans to assist with dura stripping in a GE scanner?

2013-05-10 Thread Bruce Fischl
! On Tue, May 7, 2013 at 2:24 PM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Katie I'm really not sure. These days I would recommend a highres (e.g. 1mm isotropic) FLAIR if you can get one, or T2 if not. The T2* can help, but it's pretty noisy in brain. cheers

Re: [Freesurfer] Working with MEMPRAGE

2013-05-11 Thread Bruce Fischl
sure to analyze only the RMS in recon-all (ie , that is the only volume that goes into mri/orig doug On 5/9/13 6:48 PM, Bruce Fischl wrote: Hi Kayle you would run recon-all on the RMS, then run the dura stuff posthoc. cheers Bruce On Thu, 9 May 2013, Kayle Sawyer wrote: Hi all, Can

Re: [Freesurfer] Binary volume to surface label

2013-05-12 Thread Bruce Fischl
in vol2surf? I have other labels that are larger so I would prefer not to retrace them if possible. Inline image 2 Best,  Jonathan On Sun, May 12, 2013 at 10:11 AM, Bruce Fischl fis...@nmr.mgh.harvard.edu wrote: Hi Jonathan what is the label? What space is it in? If it has gray/white

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