[Freesurfer] Using PetSurfer to derive R1 values from early-phase dynamic PET

External Email - Use Caution Hello Doug and PetSurfers, I would like to extract relative regional cerebral blood flow (R1) data from early time-interval of dynamic PET data (i.e. 11C-PiB) using the MRTM2 technique in PetSurfer. The time interval that I am interested in is betwee

[Freesurfer] Petsurfer: Longitudinal GTM stats?

External Email - Use Caution Hi Freesurfer Team and Doug, Is there any way to derive the gtmstats from Petsurfer within a longitudinal design?  Could I get your take on the steps below? 1. Extract GTM stats from each PET time-point (registered to the closest structural MRI in

[Freesurfer] Calculating subject-level voxelwise % change in cortical thickness across timepoints

External Email - Use Caution Hi Freesurfer Experts, I have a question about calculating voxelwise % change.  We have collected T1-MRI across 3 time points in a couple of subjects and the aim is to produce individual surfaces/maps showing the % of cortical thinning with respect

[Freesurfer] PetSurfer: NaNs in MGX volumes

Hi Doug, Reposting this on the FS mailing list: After MGX-PVC and MRTM2, I sometimes get NaNs in the voxelwise corrected PET data when I load it on Freeview. Error message looks like this WARNING: 19 NaNs found in volume Is this happening because the MGX GM threshold is too high (I am using 0

Re: [Freesurfer] PetSurfer: Other quantification algorithms?

be it is not > too hard. > > > On 01/25/2018 06:37 PM, Elijah Mak wrote: >> Dear Doug, >> >> In addition to the MRTM approaches, I was wondering if you have any plans to >> implement other algorithms in PetSurfer, such as supervised cluster analysis >>

[Freesurfer] PetSurfer: Other quantification algorithms?

Dear Doug, In addition to the MRTM approaches, I was wondering if you have any plans to implement other algorithms in PetSurfer, such as supervised cluster analysis for extracting reference tissue activity? I am working with [11C]PK11195 PET data (neuroinflammation), for which there is no suita

[Freesurfer] Accounting for WMHs in PETSURFER PVC?

Hi Doug, Could we tweak the PETSURFER pipeline in order to account for inhomogeneous PET activity in WM due to WMHs? Will running gtmseg with the command --keep-hypo be useful in this context? Thanks for any inputs. Best Wishes, Elijah ___ Freesurf

Re: [Freesurfer] (no subject)

t; HelpLine at > http://www.partners.org/complianceline . If the e-mail was sent to you in > error > but does not contain patient information, please contact the sender and > properly > dispose of the e-mail. > > -- Elijah Mak, Gates Scholar PhD Candi

Re: [Freesurfer] PETSURFER: MRTM2 volumes?

rh.bp.nii.gz --subject fsaverage --o smoothed.bpnd.in.volume.nii.gz The next step is to bring the volumes into CVS-MNI152 space. Mri_cvs_register has been done on the T1. Thanks Doug. Best Wishes, Elijah Dr. Elijah Mak, Research Associate Department of Psychiatry Old Age Psychiatry Group

Re: [Freesurfer] Constrain smoothing to GM for PET data

Hi Doug, I am looking for a total GM mask that includes cortical and subcortical regions. Best Wishes, Elijah Dr. Elijah Mak, Research Associate Department of Psychiatry Old Age Psychiatry Group | Cambridge Intellectual & Developmental Disabilities Research Group University of Cambr

Re: [Freesurfer] Constrain smoothing to GM for PET data

st Wishes, Elijah > On 13 Oct 2017, at 17:06, Douglas Greve wrote: > > That subcort mask is only GM (sorry, should have indicated that when I named > it). > > On 10/13/17 11:15 AM, Elijah Mak wrote: >> Hi Doug, >> >> Yes, but I am using the GM rather than

Re: [Freesurfer] PETSURFER: MRTM2 volumes?

> do you mean you want to map the surface-based data into the volume? If > so, you can use mri_surf2vol. If you want to analyze your pet data in > the volume you can just do that with mri_glmfit > > > On 10/5/17 4:59 PM, Elijah Mak wrote: >> Hi Doug, >> >&g

Re: [Freesurfer] Constrain smoothing to GM for PET data

Got it. Thanks, Doug! :) Best Wishes, Elijah > On 13 Oct 2017, at 17:06, Douglas Greve wrote: > > That subcort mask is only GM (sorry, should have indicated that when I named > it). > > On 10/13/17 11:15 AM, Elijah Mak wrote: >> Hi Doug, >> >> Yes, b

Re: [Freesurfer] Constrain smoothing to GM for PET data

Hi Doug, Yes, but I am using the GM rather than the subcortical volume. How can we get a similar GM mask on CVS 2mm space? Thanks for your help. Best Wishes, Elijah Dr. Elijah Mak, Research Associate Department of Psychiatry, Old Age Psychiatry Group | Cambridge Intellectual

Re: [Freesurfer] Normalize to mni

your analysis (assuming it is a voxelwise analysis?) to the subcortical regions? You could use the subcort.mask.mgz in fsaverage/mri.2mm as as mask in your mri_glmfit. I will leave it to Doug to confirm if those steps are suitable for your objectives. Best Wishes, Elijah Dr. Elijah Mak

Re: [Freesurfer] Constrain smoothing to GM for PET data

, use the pvf. > > On 10/4/17 9:42 AM, Elijah Mak wrote: >> Hi Doug, >> >> I have used PETSURFER to derive MGX GM volumes from PET data. Now, I would >> like to constrain the smoothing to the GM. Is it advisable to use the PVF in >> the aux folder for this

Re: [Freesurfer] Overlap between Yeo networks and aparc2009 segments

Hi Shahin, You could try binarising the Yeo atlas into individual masks for each of the networks. Then, use mri_compute_overlap to quantify the correspondence between your labels and the binarised network segments. Cheers, Elijah > On 11 Oct 2017, at 18:20, sha...@nmr.mgh.harvard.edu wrote:

[Freesurfer] PETSURFER: MRTM2 volumes?

Hi Doug, Referring to the PETSURFER tutorial for dynamic PET data, I am wondering if it is possible to obtain a volume-based equivalent of mrtm2.lh.sm05/bp.nii.gz? As I understand, bp.nii.gz is the partial-volumed corrected output that has been sampled onto the fsaverage surface. Thanks for y

[Freesurfer] Constrain smoothing to GM for PET data

Hi Doug, I have used PETSURFER to derive MGX GM volumes from PET data. Now, I would like to constrain the smoothing to the GM. Is it advisable to use the PVF in the aux folder for this purpose? If not, what is the best approach do this? Thanks! Best Wishes, Elijah __

Re: [Freesurfer] Adding control points to aparc+aseg

Hi Nicholas, In such situations, I have learned that autorecon2-wm after adding WM voxels seems to work pretty well. Hope that helps.  Best Wishes, Elijah On 27 September 2017 at 16:46:43, Nicholas Goh (ngo...@gmail.com) wrote: Bruce, Thank you for the response. Attempting to use this method

Re: [Freesurfer] PetSurfer GTM: gtmstats2table

Hi Doug, Thanks for the clarification. According to the PetSurfer guide, it is stated that there are “ways to customise this segmentation to use ROI definitions”. How may I go about doing that? Appreciate your help. Best Wishes, Elijah  Dr. Elijah Mak, Research Associate Department of

[Freesurfer] PetSurfer GTM: gtmstats2table

Hi Doug, Would it be possible to use the gtmstats2table command to extract GTM values from other parellations? Thanks! Best Wishes, Elijah Dr. Elijah Mak, Research Associate Department of Psychiatry Old Age Psychiatry Group | Cambridge Intellectual & Developmental Disabilities Rese

[Freesurfer] Gcuts erasing voxels within the ventricles

Hi Freesurfer Team, I am using gcut to improve the skull stripping on some subjects. I noticed that it is also removing some of the voxels in the ventricles of the brainmask.mgz (picture attached). Is this normal behaviour?  Thanks for your time. Best Wishes, Elijah 

[Freesurfer] Sampling vertex-wise data across various distances from the core of a mask to a somewhere else on fsaverage

Hi Doug and Freesurfer Experts, I am trying to see whether cortical thinning gets progressively less severe as we move further away from a seed/voxel (e.g. precuneus). Is it possible to perform correlations between the (a) distance between a given vertex to specific point on fsaverage, and the

Re: [Freesurfer] Extracting vertex data from thickness maps after masking by sig.mgh

; cc = MRIread('concat.mgh'); ccmat = fast_vol2mat(cc); cc_in_mask = ccmat(:,imask); On 7/31/17 10:25 AM, Elijah Mak wrote: Hi Doug, Thanks! mri_segstats —i concat.mgh  --seg mask.mgh --avgwf data 1) concat.mgh is the stack of individual surfaces in fsaverage space 2) mask.mgh is th

Re: [Freesurfer] Extracting vertex data from thickness maps after masking by sig.mgh

one time point) or --avgwf (for multiple). Pass your mask with --seg. By default it will give you both outside the mask (first column) and inside the mask (second column). On 7/28/17 10:44 AM, Elijah Mak wrote: Hi Freesurfer Team, I have previously used mri_binarize to derive the mask.mgh

[Freesurfer] Extracting vertex data from thickness maps after masking by sig.mgh

Hi Freesurfer Team, I have previously used mri_binarize to derive the mask.mgh from the sig.mgh after a first-level group comparison of cortical thickness. Now, I would like to extract the vertex data from from another modality surface within and outside the mask in individual subjects. Is ther

Re: [Freesurfer] Using asegstats2table for gtm.stats.dat?

input  gtmstats2table --f gtmdirlist --o data/gtmstats.csv Hope that helps. Best Wishes, Elijah Elijah Mak, Research Associate Department of Psychiatry,  Old Age Psychiatry Group University of Cambridge Trinity College, CB21TQ, UK http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24 

Re: [Freesurfer] Using asegstats2table for gtm.stats.dat?

Thanks Doug! It works! Best Wishes, Elijah  On 21 June 2017 at 16:09:29, Douglas N Greve (gr...@nmr.mgh.harvard.edu) wrote: use this script https://gate.nmr.mgh.harvard.edu/safelinks/greve/gtmstats2table On 06/21/2017 10:53 AM, Elijah Mak wrote: > Hi Freesurfer Team > >

Re: [Freesurfer] Using asegstats2table for gtm.stats.dat?

Hi Freesurfer Team Apologies for bumping this thread up again. I am wondering if is there is a way to extract the ROI stats in gtm.stats.dat after mri_gtmpvc (using a similar approach such as asegstats2table)? Thanks for your help! Best Wishes, Elijah On 16 June 2017 at 16:53:33, Elijah

[Freesurfer] Using asegstats2table for gtm.stats.dat?

Hi Unix experts, I am trying to extract the PVC-ed values from gtm.stats.dat for every subject. Is there a fast way to do this using a similar workflow with asegstats2table? Thanks. Best Wishes, Elijah  ___ Freesurfer mailing list Freesurfer@nmr.mgh.h

[Freesurfer] Extracting cortical PET data from T1: aparc+aseg.mgz vs surface

Hi Freesurfer team,  I am trying to extract ROI PET data from the cortical regions using the Desikan atlas, and I am wondering which is the recommended approach. 1) mri_segstats on resampled aparc+aseg.mgz in PET space or 2) mri_segstats on lh.PetSurface.mgh in native surface (not fsaverage). O

Re: [Freesurfer] Merging outputs of mri_label2vol across hemi

) voxels PVF (null) Thesholding hit volume. mri_label2vol done  Thanks. Appreciate your help. Best Wishes, Elijah  On 14 June 2017 at 16:18:24, Douglas Greve (gr...@nmr.mgh.harvard.edu) wrote: Hmmm, not sure. can you send the full terminal output? On 6/13/17 7:03 PM, Elijah Mak wrote: Hi Doug

Re: [Freesurfer] mri_vol2surf: visualising the edges at projfrac 0.1 - 0.5

Hi Freesurfer Team, No worries, I have found a helpful solution from an old thread using mris_expand. <http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg40894.html> http://i.imgur.com/CrF125X.png Thanks. Best Wishes, Elijah On Tue, Jun 13, 2017 at 8:47 PM, Elijah Mak wrote:

[Freesurfer] mri_vol2surf: visualising the edges at projfrac 0.1 - 0.5

Hi Freesurfer Team, Is there a way to visualise the sampling edges across a range of projfrac values (0.1 (closer to WM) - 0.5) and overlay them onto PET data? Any suggestions are greatly appreciated. Thanks. Best Wishes, Elijah  ___ Freesurfer mail

Re: [Freesurfer] Merging outputs of mri_label2vol across hemi

thing like mri_mask seg1.nii.gz seg2.nii.gz seg1-masked.nii.gz then use the masked in the mri_concat command On 6/11/17 11:18 AM, Elijah Mak wrote: Hi Freesurfer Team, I am trying to resample the aparc annotation into functional space using mri_label2vol. It works fine and the script produce

Re: [Freesurfer] Merging outputs of mri_label2vol across hemi

like mri_mask seg1.nii.gz seg2.nii.gz seg1-masked.nii.gz then use the masked in the mri_concat command On 6/11/17 11:18 AM, Elijah Mak wrote: Hi Freesurfer Team, I am trying to resample the aparc annotation into functional space using mri_label2vol. It works fine and the script produce

[Freesurfer] Merging outputs of mri_label2vol across hemi

Hi Freesurfer Team, I am trying to resample the aparc annotation into functional space using mri_label2vol. It works fine and the script produced the segmentation for each hemisphere. Is there a way to merge both the left and right volumes together? Thanks for your help. Best Wishes, Elijah___

[Freesurfer] mri_cvs_register error: Symbol not found: ___emutls_get_address

Hi Freesurfer Developers, I am trying use mri_cvs_register but I ran into an error (Mac OS SIERRA 10.12.2). The log is pasted below. Logfile for mri_cvs_register Sat 10 Jun 2017 17:58:48 BST --mov 16084 $Id: mri_cvs_register,v 1.48 2016/03/06 21:31:56 lzollei Exp $ dhcp-10-240-198-151.cp.wireles

Re: [Freesurfer] Regarding: Group analysis of WMHs

...@nmr.mgh.harvard.edu) wrote: On 06/09/2017 04:32 PM, Elijah Mak wrote: > Hi Doug, > > I am referring to a rather old thread where you have provided some > interesting suggestions to perform group-wise analysis of WMHs. I am > trying to do something similar in patien

Re: [Freesurfer] Regarding: Group analysis of WMHs

a few subjects. This happens despite a good-looking talairach registration. Thanks a lot for your time in advance and I’ll appreciate any thoughts you may have on this. Sincerely, Elijah Dr. Elijah Mak, Research Associate Department of Psychiatry,  Old Age Psychiatry Group University of

Re: [Freesurfer] Creating age-adjusted z score maps against a control group

you. Best Wishes, Elijah Dr. Elijah Mak, Research Associate Department of Psychiatry,  Old Age Psychiatry Group University of Cambridge Trinity College, CB21TQ, UK http://www.neuroscience.cam.ac.uk/directory/profile.php?fkm24 On 23 May 2017 at 09:21:24, Elijah Mak (fk...@medschl.cam.ac.uk) wrote

Re: [Freesurfer] Question - multiple comparisons in FS versus SPSS

Hi Siri, Are you trying to overlay the p value associated with each region on the fsaverage surface? This may help: http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg50465.html Best Wishes, Elijah  Dr. Elijah Mak, Research Associate Department of Psychiatry,  Old Age Psychiatry

[Freesurfer] Creating age-adjusted z score maps against a control group

adjust the Z score maps for age, and then produce an age-adjusted Z score map? Thanks for your help. Best Wishes, Elijah Dr. Elijah Mak, Research Associate Department of Psychiatry,  Old Age Psychiatry Group University of Cambridge Trinity College, CB21TQ, UK http://www.neuroscience.cam.ac.uk

Re: [Freesurfer] Hyperintensities Volume ?

Hi, Not that I'm aware of. You could use the WM Hypointensities label from aseg though. Despite its understimation of WMH, we have actually found a high correlation with WMH segmented from FLAIRS in over 100 elderly and demented subjects (r < 0.8). Cheers, Elijah Dr. Elijah Mak,

Re: [Freesurfer] Thresholding sig.mgh with cluster extent K > 20 voxels

Thanks Doug. Just to confirm do I get this voxels number from the cluster summary text file then? Best Wishes, Elijah Dr. Elijah Mak, Research Associate Department of Psychiatry,  Old Age Psychiatry Group University of Cambridge Trinity College, CB21TQ, UK http://www.neuroscience.cam.ac.uk

[Freesurfer] Thresholding sig.mgh with cluster extent K > 20 voxels

Hi Everyone, How may I threshold the sig.mgh (p<0.001) with a cluster extent K > 20 voxels? Is it possible to do this in Freesurfer? Thanks. Best Wishes, Elijah Dr. Elijah Mak, Research Associate Department of Psychiatry,  Old Age Psychiatry Group University of Cambridge Trinity C

[Freesurfer] Extracting fMRI mean time series from Desikan ROIs

your help. Thanks! Best Wishes, Elijah  Elijah Mak, Research Associate Department of Psychiatry,  Old Age Psychiatry Group University of Cambridge Trinity College, CB21TQ, UK ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] Worse determination of ?h.white with v6.0 in comparison to v5.3 - worse GM/WM contrast

Hi, I've also come across similar situations in my FS 6.0 dataset. I have tried tweaking the seg-wlo and seg-ghi values and these steps have led to marked improvements in some cases. Curious to hear from the FS team too. Thanks. Best Wishes, Elijah Elijah Mak, Research Asso

Re: [Freesurfer] PCA on PET / Thickness in Freesurfer

Hi Doug, Thanks. It works! What does each vertex represent in V.mgh? http://imgur.com/W1RZdKn Here are the results from the stats. Then, I would like to extract the 1st component and convert it into label for mri_segstats. How may I do that? 1 105131.57 105131.5773.79 73.79 2913

Re: [Freesurfer] Cohen's D = gamma.mgh / rstd.mgh?

Hi Doug, This is my main objective. 1. PET in Group 1 vs Group 2 2. Thickness in the same sample, Group 1 vs Group 2 3. ASL in the same sample of Group 1 vs Group 2 4. Create a binary mask of the overlapping corrected sig voxels from 1-3. 5. This mask is therefore a site of co-localised atrophy,

Re: [Freesurfer] Cohen's D = gamma.mgh / rstd.mgh?

Dear Doug, Thanks. Do you mean use ROI averages as the samples and then test across ROIs? This would be unusual as the interpretation is problematic. I would probably compute a single number per subject that is a weighted sum/difference of the ROI values, then test whether this one number is d

[Freesurfer] Cohen's D = gamma.mgh / rstd.mgh?

Hi there, What is the correct way to plot, at each vertex, the Cohen's *D* after a *mri_glmfit* comparison? I've seen a few variations posted on the mailing list. Is gamma.mgh / rstd.mgh is the correct formula? Does rstd.mgh represent pooled SD across both groups (patients and controls)? Secondl

Re: [Freesurfer] ASL processing in Freesurfer?

Apologies, please ignore the other email response. I believe this should be tagged to the right thread (hopefully!) - Many thanks for the information, Doug! I will give it a go. Actually, I would like to carry out the following analyses: Get regional estimates of perfusion within a region o

Re: [Freesurfer] ASL processing in Freesurfer? (Douglas Greve)

Many thanks for the information, Doug! I will give it a go. Actually, I would like to carry out the following analyses: Get regional estimates of perfusion within a region of interest as defined by a significant cluster after mri_glmfit-sim. as well as other cortical regions that are connected to

[Freesurfer] Freesurfer 6 beta testing: mri_glmfit-sim error

Hi Freesurfer Team, I came across the following error while running mri_glmfit-sim. What is vwsigmax? Thanks for your help again. The full log is as follows: $Id: FreeSurferEnv.csh,v 1.89 2016/06/09 14:54:31 zkaufman Exp $ Sat Nov 19 02:00:45 GMT 2016 Darwin dhcp-10-240-201-24.cp.wireless.privat

Re: [Freesurfer] [Announcement] Freesurfer v6.0 beta release and testing

Hi ZK, Thanks. It is great news! I would like to report the following. asegstats2table seems to be acting strangely. File "/Applications/freesurfer_b6/bin/asegstats2table", line 195 print 'ERROR: subjects are not specified (use --subjects SUBJECTS)' Even typing asegstats2table --help lead

Re: [Freesurfer] Comparing z score maps between 2 modalities in a group?

, and both modalities (PET and T1) were Z-scored relative to controls, and then compared against each other. Best Wishes, Elijah On Fri, Nov 18, 2016 at 5:24 PM, Elijah Mak wrote: > Hi Doug, > > Thanks for taking a look at the commands! > > I would like to ask a further ques

Re: [Freesurfer] Extracting structural measures from trend-level PET clusters

of emails here and can't keep track of each person's issue. thanks! doug On 11/11/2016 08:06 PM, Elijah Mak wrote: > Hi, > > A bit more info: the stack of thickness maps consists of > lh.thickness.fwhm15.fsaverage.mghs that were created after -qcache. I > used mri_concat -

[Freesurfer] Comparing z score maps between 2 modalities in a group?

Hi Freesurfer Team, We would like to compare Z-scored surface maps between different modalities (MRI and PET) within a single group. 1 subject = 2 measures. These are my steps so far, using mri_concat and fscalc for the generation of the Z score maps. Differences between Z-score maps are tested u

Re: [Freesurfer] Extracting structural measures from trend-level PET clusters

mghs are in the expected range. Should I be using this for the calculation of the thickness in the clusters instead? Best Wishes, Elijah On Sat, Nov 12, 2016 at 12:15 AM, Elijah Mak wrote: > Thanks, Doug. > > It works but I am not sure if the values I'm getting are correct. Is this

Re: [Freesurfer] Extracting structural measures from trend-level PET clusters

Thanks, Doug. It works but I am not sure if the values I'm getting are correct. Is this supposed to be reporting the mean cortical thickness of each cluster? I have pasted the output below from the avgwf below. The names of the clusters correspond to the regions from the "summary" text, am I righ

[Freesurfer] How to view overlapping voxels across multiple sig.mgh files?

Hi Freesurfer Team, I am just wondering if there is a neat way to derive .mgh files containing cluster information about spatially overlapping voxels across various sig.mgh? Thank you. Best Wishes, Elijah ___ Freesurfer mailing list Freesurfer@nmr.mgh.

[Freesurfer] Extracting structural measures from trend-level PET clusters

Hi Freesurfer Team, 1) We've found some subtle differences in tau accumulation between two groups. Unfortunately, it does not survive mri_glmfit-sim (voxel threshold 0.001, cwp < 0.05). Still, I would like to extract the structural measures from the uncorrected tau clusters (p<0.001). What is the

Re: [Freesurfer] Assessing local correlations across 2 modalities

Hello, Thanks Doug for your help on this previously. I am quite puzzled by the vertex-wise local correlations that I've found (i.e more tau thicker cortex)... and before I go down the rabbit hole of trying to dissect what could be happening, I'd like to check if one of the steps in my workflow ha

[Freesurfer] latest version of mri_glmfit-sim?

H ello Freesurfer Team, Where may I download the latest version of mri_glmfit-sim and QDEC to run the mri_surfcluster? I am having errors on mri_glmfit-sim and monte-carlo simulations in QDEC (dev version that was

Re: [Freesurfer] BBR not recommended for PETSurfer?

Hi Christopher, We have very positive experiences with mri_coreg too. http://www.mail-archive.com/freesurfer@nmr.mgh.harvard.edu/msg47135.html Quite a bit of manual tweaking had to be done along with BBR for our AV and PK BPnd data. It works just fine on the PIB SUVRs though. Then, we switched

Re: [Freesurfer] Visualising path.mean.txt in MNI space after trac-all -stat

Hi Anastasia, Yes indeed. I am using a dev version of freeview. I could give it another go with the freeview that came with v5.3. But does this mean that I shoudl also I re-run the tracula -stat on a v5.3? Thanks! Best Wishes, Elijah ___ Freesurfer mai

[Freesurfer] Visualising path.mean.txt in MNI space after trac-all -stat

Hi Anastasia and others, I am trying to visualise the *.path.mean.txt on MNI template after running trac-all -stat. I used this command: freeview -v $FSLDIR/data/standard/MNI152_T1_1mm_brain.nii.gz -w stats/*.path.mean.txt However, it looks like something has gone wrong with the labelling and po

Re: [Freesurfer] TRACULA - difference in tracts using MNI vs CVS

? Thanks for your patience :) Best Wishes, Elijah -- Elijah Mak, Gates Scholar PhD Candidate *|* Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https

Re: [Freesurfer] TRACULA - difference in tracts using MNI vs CVS

in the Neuroimage paper: where a subject was excluded if there were failures of reconstruction in 2 or more WM tracts. Thank you for your help! Best Wishes, Elijah -- Elijah Mak, Gates Scholar PhD Candidate *|* Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ

Re: [Freesurfer] TRACULA - difference in tracts using MNI vs CVS

Dear Anastasia, I have also uploaded the file with the problem (22995_EM.zip), and this is how my config file looks like after modifications: set subjlist = (22995) set pathlist = (fmajor_PP) set ncpts = (7) set reinit = (1) Thanks again! Best Wishes, Elijah -- Elijah Mak PhD Candidate

[Freesurfer] Assessing local correlations across 2 modalities

way in Freesurfer to properly address this? My PET data have already been registered and projected to the surfaces for each individual. Thanks a lot. Best Wishes, Elijah -- Elijah Mak PhD Candidate *|* Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ

Re: [Freesurfer] WM Hyperintensities

tners.org/complianceline . If the e-mail was sent to you in error but does not contain patient information, please contact the sender and properly dispose of the e-mail. -- Elijah Mak, Gates Scholar PhD Candidate *|* Psychiatry University of Cambridge Trinity College, Cambridge, CB2 1TQ

[Freesurfer] mri_coreg !

urriness can throw BBR > off a bit. What kind of PET data do you have? > > > On 05/16/2016 03:06 PM, Elijah Mak wrote: >> Hi Doug, >> >> I just want to say that mri_coreg worked tremendously well for the >> registration of some very blurry PET-PK data. I wa

[Freesurfer] mri_coreg !

Hi Doug, I just want to say that mri_coreg worked tremendously well for the registration of some very blurry PET-PK data. I was not getting any success with bbregister and init-fsl or mri_robust_register options. How does this technique differ from the boundary-based registration? Thanks a lot.

Re: [Freesurfer] PET voxelwise & Segmentation Fault during mri_glmfit-sim

No, more like running the voxelwise comparisons only on voxels that have positive BP between 2 group. Is that possible? On another note, I am running into a puzzling "Segmentation fault" error with the following command: mri_glmfit-sim --glmdir lh_ad_hc.glmdir --cache 2 neg --cwp 0.05 --2spac

[Freesurfer] REPOST: TRACULA dev version: Error message

Hi Freesurfer, Sorry about reposting this email from earlier: I can't seem to get the TRACULA in the dev version of FS6 to run. mv -f /Users/MacPro/Documents/NIMROD_DTI/SUBJECT/dmri/dwi_orig_flip.mghdti.bvecs /Users/MacPro/Documents/NIMROD_DTI/SUBJECT/dmri/bvecs mv: rename /Users/MacPro/Documen

Re: [Freesurfer] PET voxelwise

Dear Doug, One more question: There are many voxels with negative binding potentials in this dataset, mostly in the CSF/ventricular regions. Can I restrict the mri_glmfit to focus only on the voxels with positive BP? Best Wishes, Elijah ___ Freesurfer

Re: [Freesurfer] PET voxelwise

header)" Using this method, I realise I could simply specify -regheader without feeding the .lta for mri_vol2surf and it seems to work well. Best Wishes, Elijah How did you edit the registration? Does it work with the unedited version? On 04/13/2016 10:21 AM, Elijah Mak wrote: > Hi Do

Re: [Freesurfer] Viewing eroded structure after -seg-erode 1

Also make sure to set the threshold to something like 0.5 On 04/11/2016 09:41 AM, Elijah Mak wrote: > Hi Freesurfer Community, > > I have performed -seg-erode 1 during mri_segstats on resampled > subcortical strutures (T1 to FA/MD). Can I view the eroded masks in T1 > anatomical space

Re: [Freesurfer] PET voxelwise

Hi Doug, One more question about feeding the -reg to mri_vol2surf, please. I am specifying the registration .lta because I have made edits to it, mri_vol2surf --src FS6_24551_MPRAGE_Neuro.nii/pet/pet2free_fsl.mgz --out FS6_24551_MPRAGE_Neuro.nii/surf/lh.PETSurfce.mgh --projfrac 0.5 --hemi lh --r

[Freesurfer] TRACULA dev version: Error message

Hi Freesurfer Community, I am running TRACULA on a single subject in the dev version (freesurfer-Darwin-OSX-stable-v6-beta-20151015) #- /Applications/freesurfer6beta/bin/trac-preproc #- #@# Image corrections Mon Apr 11 16:

Re: [Freesurfer] Viewing eroded structure after -seg-erode 1

Thanks Doug. Do you mean loading the structure (i.e. LeftHippocampus2diff.mgz) on the orig.mgz as an overlay? I am able to do that but I can't seem to find an option for thresholding. Sorry if I misunderstood your original email. Best Wishes, Elijah ___

[Freesurfer] Viewing eroded structure after -seg-erode 1

Hi Freesurfer Community, I have performed -seg-erode 1 during mri_segstats on resampled subcortical strutures (T1 to FA/MD). Can I view the eroded masks in T1 anatomical space to visually inspect whether PVE has been adequately accounted for? Thank you. Best Wishes, Elijah __

Re: [Freesurfer] FA and MD *positively* correlated within same regions ?

Hi Kirstie, Yes indeed there were 3 subjects at the bottom-left of the plot. To account for PV, I eroded the boundaries using *-seg-erode 1* during the *mri_segstats* stage, and this resulted in a few subjects with no data for the WM entorhinal region (although these were saved as "0" in the .sta

Re: [Freesurfer] FA and MD *positively* correlated within same regions ?

Hi Alshikho , Yes, I am sure :) Same sequence for everyone. Just to add. FA and MD were significantly negatively correlated for the other regions including the fusiform, precuneus, hippocampu

Re: [Freesurfer] Cortical thickness average

Hi Sahil, I did something similar recently. I believe you can use mri_concat with the -mean option to create an average map of the group. Another option might be make_average_subject? https://surfer.nmr.mgh.harvard.edu/fswiki/make_average_subject Best Wishes, Elijah

[Freesurfer] FA and MD *positively* correlated within same regions ?

Hi Freesurfer Community, I recently used mri_segstats to extract FA and MD as suggested here: http://freesurfer.net/fswiki/FsTutorial/Diffusion Using the aparc+aseg and wmparc (resampled to diffusion space), I looked at some of the correlations between FA and MD in the same regions, and came acro

Re: [Freesurfer] PET voxelwise

mri_concat --f pib_lh_fsaverage (textfile of subjects and their images) --o concat_lh_pet.mgh Should I add -mean here for the GLM? mri_glmfit --y concat_lh_pet.mgh --fsgd pib_fsgd --C group1.group2.mtx --surf fsaverage lh --cortex --glmdir lh.pet.glmdir My simple 2 group-no-covariates FS

Re: [Freesurfer] PET voxelwise

Hi Doug, Thanks! I manually tweaked the registration of the PET to T1 on a number of subjects to bring the mincost down to < 0.5. After saving the pet2free volume in Freeview, I noticed that a new .lta is produced in the same directory (i.e. pet2free_fsl.mgz.lta). Will the option --regheader te

[Freesurfer] PET voxelwise

Hi Freesurfer Community, I am trying to run a vertex-wise analyses of PET data. I have already performed bbregister. Next, I did mri_vol2surf for each subject, left and right hemispheres. for i in `cat subjects`; do mri_vol2surf --src FS6_${i}_MPRAGE_Neuro.nii/pet/pet2free_fsl.mgz --out FS6_${i}

[Freesurfer] mri_cvs_register : output

Hi Freesurfer Community, I am running mri_cvs_register for the spatial normalization and it seems to work very nicely on my set of DTI data in subjects with substantial atrophy. However, I can't seem to find the file combined_tocvs_avg35_elreg_afteraseg-norm.m3z, however, I have final_CVSmorph_to

Re: [Freesurfer] Reading values from overlays with PETcoreg

Dear Doug, Is it possible to use BP SUVR PET that have been registered to T1 for this gtmseg workflow? You mentioned that the mean TAC should be used as the input. 2 quick questions: What's mean TAC and why? Thanks. Best Wishes, Elijah ___ Freesurfer m

[Freesurfer] General diffusion workflow questions: QC and extracting FA from subcortical structures

bjectname/dtrecon/fa-masked_aparcaseg.mgz --seg-erode 1 --sum subjectname/stats/fa_aparc+aseg2diff_segerode_1;done Thanks a lot for your time and help! Best Wishes, Elijah -- Elijah Mak PhD Candidate *|* Psychiatry University of Cambridge Trinity College

Re: [Freesurfer] Extracting MNI Coordinates from the Destrieux Atlas: Checking steps

ported in mni305 coords. On 08/10/2015 08:39 AM, Elijah Mak wrote: > Hi Freesurfer Experts, > > For the purpose of defining nodes in a graph theory analysis, I would > like to generate a list of X Y Z coordinates in MNI space for all the > labels in the Destrieux atlas. I came

Re: [Freesurfer] Extracting MNI Coordinates from the Destrieux Atlas: Checking steps

-22.0 17.4 163842 13.533 117158 82219.39-29.4 -22.0 17.4 163842 13.170 83424 82219.39-29.4 -22.0 17.4 163842 The same thing happens to the ROIs on the RH (XYZ: 29.8 29.8 18.0). Best Wishes, Elijah -- Elijah Mak, Gates Scholar PhD Candidate

[Freesurfer] Extracting MNI Coordinates from the Destrieux Atlas: Checking steps

) # FixMNI = 1 # # ClusterNo Max VtxMax Size(mm^2) TalX TalY TalZNVtxs 13.332 83949 82219.39-29.4 -22.0 17.4 163842 Are those TalX TalY TalZ the values I'm looking for? Many thanks for your time. Best Wishes, Elijah -- Elijah Mak, PhD Cand

[Freesurfer] FS6 DEV Hippocampal Subfield Error

28 00:34:01 BST 2015 Ended at Thu May 28 00:34:04 BST 2015 #@#%# recon-all-run-time-hours 0.001 recon-all -s JT_D372A_3D_A finished without error at Thu May 28 00:34:05 BST 2015 Any help is greatly appreciated, many thanks! Best Wishes, Elijah -- Elijah Mak, PhD Candidate *|* Psychiatry Uni

[Freesurfer] FS6 Dev: recon-all error

133 ERROR: mpr2mni305 execution aborted Any idea what is happening? There were no such problems in the recon-all with the earlier v5.3 build. Thanks a lot for your help. Best Wishes, Elijah -- Elijah Mak, Gates Scholar PhD Candidate *|* Psychiatry University of Cambridge Trinity College, Cambridg

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