Re: [Freesurfer] cortical thickness group analysis

: freesurfer@nmr.mgh.harvard.edu Subject: [Freesurfer] cortical thickness group analysis External Email - Use Caution Hello, I am trying to run a group analysis on cortical thickness (two groups, no covariates). I have been trying to follow the tutorial (FsTutorialGroupAnalysis) but I

[Freesurfer] cortical thickness group analysis

External Email - Use Caution Hello, I am trying to run a group analysis on cortical thickness (two groups, no covariates). I have been trying to follow the tutorial (FsTutorialGroupAnalysis) but I run into a problem with the mri_glmfit. My script looks like this: fspath="/dat/fre

[Freesurfer] Cortical Thickness Extraction after Dura Correction with Multi-echo MPRAGE

External Email - Use Caution Hello Freesurfer experts, I am interested in using Freesurfer 7.3.2 to extract cortical thickness values from multi-echo MPRAGE data. I ran recon-all using the T1 RMS and T2 images, and then I ran dura correction using the four T1 echo images to create

Re: [Freesurfer] cortical thickness measurements

External Email - Use Caution Hi, I am trying to determine which imaging type is ideal for cortical segmentation and thickness measurement: MPRAGE, MP2RAGE, or MEMP2RAGE on a 3T Philips scanner. Any helpful comments would be greatly appreciated. Thank you AJ ___

Re: [Freesurfer] Cortical Thickness Measurement in Cortical Lesion ROI

You should load $chronic_CMI_volume_path/"$sub_base"_chronic-CMI_4-1.nii.gz into freeview with the surfaces, eg cd subject/mri freeview nu.mgz $chronic_CMI_volume_path/"$sub_base"_chronic-CMI_4-1.nii.gz -f ../surfs/?h.white ../surfs/?h.pial and see if the lesion maps between the white and pia

[Freesurfer] Cortical Thickness Measurement in Cortical Lesion ROI

External Email - Use Caution Dear Freesurfer Experts, I am currently engaged in a project where I need to measure the cortical thickness of a segmented cortical lesion (ROI) in the volume space. After running recon-all for my subjects, i employed 'mri_vol2surf' function to

[Freesurfer] Cortical Thickness Measurement in Cortical Lesion ROI

External Email - Use Caution Dear Freesurfer Experts, I am currently engaged in a project where I need to measure the cortical thickness of a segmented cortical lesion (ROI) in the volume space. After running recon-all for my subjects, i employed 'mri_vol2surf' function to

Re: [Freesurfer] Cortical thickness of elephant brain

uot; Sent: Wednesday, May 24, 2023 3:46:35 PM Subject: Re: [Freesurfer] Cortical thickness of elephant brain External Email - Use Caution Can you try using lh.thickness.mgz instead of just lh.thickness? On 5/23/2023 1:12 PM, Malav Shah wrote: External Email - Use Caution Hi there,

Re: [Freesurfer] Cortical thickness of elephant brain

t; *To: *"Freesurfer support list" *Sent: *Monday, May 22, 2023 5:35:56 PM *Subject: *Re: [Freesurfer] Cortical thickness of elephant brain External Email - Use Caution Thank you for a swift reply, Doug. Upon running the command "mris_diff --debug --min-dist lh.pial.5smth

Re: [Freesurfer] Cortical thickness of elephant brain

2 Segmentation fault: 11 Any suggestions? Thanks in advance, malav From: "Malav Shah" To: "Freesurfer support list" Sent: Monday, May 22, 2023 5:35:56 PM Subject: Re: [Freesurfer] Cortical thickness of elephant brain External Email - Use Caution Thank you for a

Re: [Freesurfer] Cortical thickness of elephant brain

External Email - Use Caution Hi Malav, try mris_diff --min-dist lh.wm.smth5 lh.pial.smth5 1 lh.thickness The output will be on the pial surface. Reverse the surface order to get it on the white surface doug On 5/22/2023 5:48 AM, Malav Shah wrote: External Email - Use

[Freesurfer] Cortical thickness of elephant brain

External Email - Use Caution Dear freeSurfer team, I am trying to extract cortical thickness in a postmortem elephant (structural) MRI scan. I initiated the process with the segmentation of white (wm) and pial matter, using MATLAB image processing tools. Having satisfied whit

Re: [Freesurfer] cortical thickness and z-scores correlation

The easiest thing is probably just to use matlab to load in the data (MRIread.m) and pull out the vertices you need. Alternatively, you can convert an mgh/mgz file to ascii  with mri_convert --ascii or --ascii+crsf and then do what you want with it. On 3/21/2023 12:38 PM, Maria Czarnecka wrote

[Freesurfer] cortical thickness and z-scores correlation

External Email - Use Caution Dear Sisters and Brothers in neuroscience I am a huge fan but a very new user of the freesurfer, please treat me as such when answering this email. I have successfully performed anatomical and functional data analysis using fmriprep, freesurfer and fs

Re: [Freesurfer] cortical thickness in frontal lobe

you should weight by the number of vertices in each roi On 11/9/2022 8:01 AM, James Brown wrote: External Email - Use Caution Dear Freesurfer experts, We are new to Freesurfer. We appreciate your help & apologize if the question is simple. We need cortical thickness in lobes instead o

[Freesurfer] cortical thickness in frontal lobe

External Email - Use Caution Dear Freesurfer experts, We are new to Freesurfer. We appreciate your help & apologize if the question is simple. We need cortical thickness in lobes instead of parcellates. Is it correct to take the average of the parcelates from the aparc+aseg.stats f

[Freesurfer] Converting Freesurfer Cortical Thickness Output into 32K space

External Email - Use Caution Hi, Just wondering if anyone has any experience with converting freesurfer cortical thickness output into 32K space (or native space/164k space/96k space) and can share the script you use to do it? Thanks so much! Ariana Fei

Re: [Freesurfer] Cortical Thickness measures using different ways of processing

those look like hcp commands so you should contact them On 7/28/2022 2:00 PM, Ariana Fei wrote: External Email - Use Caution I'm attaching a list of command I used to convert freesurfer cortical thickness output to native space: $Caret5_Command -file-convert -

Re: [Freesurfer] Cortical Thickness measures using different ways of processing

External Email - Use Caution I'm attaching a list of command I used to convert freesurfer cortical thickness output to native space: $Caret5_Command -file-convert -fsc2c "$FreeSurferFolder"/surf/"$hemisphere"h.thickness "$FreeSurferFol

Re: [Freesurfer] Cortical Thickness measures using different ways of processing

how are you converting them? On 7/27/2022 11:20 AM, Ariana Fei wrote: External Email - Use Caution Hi, We are recently trying to get cortical thickness from freesurfer and converting them to 32k. A problem we notice is that after converting to 32k, all the cortical thickness values

[Freesurfer] Cortical Thickness measures using different ways of processing

External Email - Use Caution Hi, We are recently trying to get cortical thickness from freesurfer and converting them to 32k. A problem we notice is that after converting to 32k, all the cortical thickness values become negative. However, when we load freesurfer thickness files in

Re: [Freesurfer] Cortical thickness difference as vertex-label overlay

] Cortical thickness difference as vertex-label overlay Try mri_mask yourcontrast/gamma.mgh sig.masked.mgh yourcontrast/gamma.masked.mgh gamma is the contrast value (eg, patients minus controls). Is that what you wnat? On 9/10/2021 6:20 AM, Graterol Pérez, José Alberto wrote: External Email

Re: [Freesurfer] Cortical thickness difference as vertex-label overlay

Try mri_mask yourcontrast/gamma.mgh sig.masked.mgh yourcontrast/gamma.masked.mgh gamma is the contrast value (eg, patients minus controls). Is that what you wnat? On 9/10/2021 6:20 AM, Graterol Pérez, José Alberto wrote: External Email - Use Caution Hello, I've done a group compari

[Freesurfer] Cortical thickness difference as vertex-label overlay

External Email - Use Caution Hello, I've done a group comparison between patients and controls, and obtained some significant cortical thickness (CT) clusters. Is there a way to obtain an overlay similar to the sig.masked, but for the vertex-wise CT values instead of the p val

Re: [Freesurfer] FreeSurfer cortical thickness

External Email - Use Caution Hi Rosie, For cortical thickness, check out *.aparc.*.stats files (e.g, lh.aparc.stats, lh.aparc.a2009s.stats, lh.aparc.DKTatlas.stats). There is more info in the ROI analysis tutorial: - https://secure-web.cisco.com/15BXH9iwkvAUJ2mnf7udx7SdsKrQQYNr

[Freesurfer] FreeSurfer cortical thickness

External Email - Use Caution Dear Freesurfer's experts, I run FreeSurfer and I got the following stats: rosalia@rosalia-Lenovo-Y520-15IKBN /media/rosalia/Nuevo_vol/ARTICO/derivatives/freesurfer/sub-003/stats $ ls aseg.stats lh.BA_exvivo.thresh.stats rh.aparc.stats

[Freesurfer] Cortical Thickness Measures for MTL

External Email - Use Caution Hello, I have been manually tracing the entorhinal cortex, dividing it into the antero-lateral entorhinal and posterior-medial entorhinal cortex. I am looking for a way to get cortical thickness measures for this region. I have a few questions relat

Re: [Freesurfer] Cortical thickness on version 6 vs 7

I have not seen anything of that magnitude. I do see a systematic drop in the thickness with v7 relative to v6, but it is on the order of 1 or 2%. It might be something specific to the pulse sequence that you are using. Try looking at the surfaces of the subject that has the largest discrepancy

Re: [Freesurfer] Cortical thickness on version 6 vs 7

the HCP Pipelines for now. We usually quote 2.6mm average cortical thickness for young adults, but it does depend on age. Matt. From: on behalf of Xiaojiang Yang Reply-To: Freesurfer support list Date: Friday, March 12, 2021 at 10:29 AM To: Freesurfer support list Subject: [Freesurfer] Cortical

Re: [Freesurfer] Cortical thickness on version 6 vs 7

2.6mm average cortical thickness for young adults, but it does depend on age. Matt. From: on behalf of Xiaojiang Yang Reply-To: Freesurfer support list Date: Friday, March 12, 2021 at 10:29 AM To: Freesurfer support list Subject: [Freesurfer] Cortical thickness on version 6 vs 7

[Freesurfer] Cortical thickness on version 6 vs 7

External Email - Use Caution Dear Freesurfer developers, I have a cohort of subjects that are already run under FS 6. I recently upgraded Freesurfer from 6.0 to 7.1.1, and now I also have run these subjects under FS 7. When comparing the cortical thickness results obtained from F

Re: [Freesurfer] cortical thickness values for each point in a ctx label file

, Donald N. *Sent:* Thursday, February 11, 2021 1:16 PM *To:* Freesurfer support list *Subject:* Re: [Freesurfer] cortical thickness values for each point in a ctx label file *External Email - Use Caution * Thanks for getting back so quickly, Doug. Creating pial label files will enable me

Re: [Freesurfer] cortical thickness values for each point in a ctx label file

between the white and pial vertex with the same label as a cortical thickness? From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Krieger, Donald N. Sent: Thursday, February 11, 2021 1:16 PM To: Freesurfer support list Subject: Re: [Freesurfer] cortical thickness values for each point in a

Re: [Freesurfer] cortical thickness values for each point in a ctx label file

tical thickness. From: freesurfer-boun...@nmr.mgh.harvard.edu On Behalf Of Douglas N. Greve Sent: Thursday, February 11, 2021 1:04 PM To: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] cortical thickness values for each point in a ctx label file Not sure what you mean as the pial file

Re: [Freesurfer] cortical thickness values for each point in a ctx label file

Not sure what you mean as the pial files are surfaces not labels or annotations. If you want to extract labels from the annotations you can use mri_annotation2label On 2/11/2021 12:55 PM, Krieger, Donald N. wrote: External Email - Use Caution Dear freesurfer group, I wish to measure

[Freesurfer] cortical thickness values for each point in a ctx label file

External Email - Use Caution Dear freesurfer group, I wish to measure a cortical thickness value for each entry in a label file, e.g. SubNo/wmparc/ctx-lh-lateraloccipital_1011.label . Is there a function in the freesurfer distribution which includes this capability? Also, is the

Re: [Freesurfer] cortical thickness ROI

Yes, you can use mris_apply_reg to map the label/annotation back to the individual, then mri_label2vol to map it into the DTI space, then use mri_segstats to extract the mean value from the ROI On 2/1/2021 1:15 PM, Sara Lyn wrote: External Email - Use Caution Hi Freesurfer developers

[Freesurfer] cortical thickness ROI

External Email - Use Caution Hi Freesurfer developers, I wanted to know if I could use an ROI obtained from cortical thickness group analysis to obtain FA values from that same ROI for each of the subjects. Appreciate any guidance, thank you. Sincerely, Sara _

Re: [Freesurfer] Cortical thickness volume ROI to surface {Disarmed}

Have you checked that the output of each of the stages is correct? Eg, does mydata_T1.nii.mgz overlay with MNI152 and with ROI_MNI? At the end of fslregister, there will be a tkregister command to visualize the regsitration. Do those look ok? On 11/17/2020 4:48 AM, Alina Rojas wrote: E

Re: [Freesurfer] Cortical thickness volume ROI to surface {Disarmed}

External Email - Use Caution Thank you for your response! Here the commands: #register image to MNIspace flirt -in mydata_T1.nii.gz -ref fsl/data/standard/MNI152_T1_1mm -out mydata_T1_MNI.nii.gz -omat mydata_T1_MNI.mat #Create a registration from the ROI-anatomical volume to a f

Re: [Freesurfer] Cortical thickness volume ROI to surface {Disarmed}

please send the command line On 11/16/2020 7:20 AM, Alina Rojas wrote: External Email - Use Caution Hello Freesurfer experts, I am attempting to register a ROI (.nii) to the surface of fsaverage to get the statistical output on the cortical thickness. I followed your instructions on

[Freesurfer] Cortical thickness volume ROI to surface {Disarmed}

External Email - Use Caution Hello Freesurfer experts, I am attempting to register a ROI (.nii) to the surface of fsaverage to get the statistical output on the cortical thickness. I followed your instructions on https://secure-web.cisco.com/1vMR3HBqveQVdV1izVoGaJ5VcRtbR7HBn6ADo

Re: [Freesurfer] cortical thickness

e, then average them (all in mm) > > -Original Message- > From: freesurfer-boun...@nmr.mgh.harvard.edu > On Behalf Of Nasiriavanaki, Zahra > Sent: Monday, July 6, 2020 1:00 PM > To: Freesurfer support list > Subject: Re: [Freesurfer] cortical thickness > > Than

Re: [Freesurfer] cortical thickness

ehalf Of Nasiriavanaki, Zahra Sent: Monday, July 6, 2020 1:00 PM To: Freesurfer support list Subject: Re: [Freesurfer] cortical thickness Thanks for your response Bruce. Does FS calculate the distance between the surface and CSF border in Euclidean and then converts it into mm? Thanks Mona >

Re: [Freesurfer] cortical thickness

mr.mgh.harvard.edu > On Behalf Of Nasiriavanaki, Zahra > Sent: Monday, July 6, 2020 12:31 PM > To: Freesurfer support list > Subject: [Freesurfer] cortical thickness > > Hi Freesurfer experts > > I have a question about the way FS calculates cortical thickness and I >

Re: [Freesurfer] cortical thickness

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

[Freesurfer] cortical thickness

Hi Freesurfer experts I have a question about the way FS calculates cortical thickness and I appreciate if you could please respond. I calculated the cortical thickness using read_curv script in a specific ROI in parietal lobe. The mean thickness at that area was 2.4. Does this number show the

Re: [Freesurfer] Cortical thickness measure for external analysis.

you should be fine with the subject metrics we generate. Typically thickness doesn't need much if any eTIV correction On Thu, 23 Apr 2020, Miguel Ángel Rivas Fernández wrote: External Email - Use Caution Dear Freesurfer experts, We are interested in running external analysis

[Freesurfer] Cortical thickness measure for external analysis.

External Email - Use Caution Dear Freesurfer experts, We are interested in running external analysis with thickness measurements of two brain regions. Can we use safely the metrics exported or by contrary a previous transformation is required before export the stats of each subjec

Re: [Freesurfer] Cortical thickness values on a vertex base level

Best wishes, > AIcha > > *Van:* freesurfer-boun...@nmr.mgh.harvard.edu > namens Greve, Douglas > N.,Ph.D. > *Verzonden:* donderdag 31 oktober 2019 19:16 > *Aan:* freesurfer@nmr.mgh.harvard.edu > *Onderwerp:* Re: [Freesurfer] Cortical thickness values on a verte

Re: [Freesurfer] Cortical thickness values on a vertex base level

31 oktober 2019 19:16 Aan: freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] Cortical thickness values on a vertex base level You can run mri_surfcluster with your fdr threshold as the --thmin value. This will output cluster number (ocn) map. This will assign the cluster number to a

Re: [Freesurfer] Cortical thickness values on a vertex base level

> > ? > > > > 0.001 > > Right parahippocampal gyrus > > > > ? > > > > ? > > > > ? > > > > 0.002 > > > Does this clarify my question? > > Best wishes, > Aicha > >

Re: [Freesurfer] Cortical thickness values on a vertex base level

, Douglas N.,Ph.D. Verzonden: donderdag 31 oktober 2019 16:25 Aan: freesurfer@nmr.mgh.harvard.edu Onderwerp: Re: [Freesurfer] Cortical thickness values on a vertex base level I'm not sure what you mean. Do you want the mean thickness of a cluster and/or its surface area? On 10/30/19 6:

Re: [Freesurfer] Cortical thickness values on a vertex base level

I'm not sure what you mean. Do you want the mean thickness of a cluster and/or its surface area? On 10/30/19 6:02 PM, Aicha Dijkshoorn wrote: > > External Email - Use Caution > > Dear developers, > > For a case-control study we are comparing the cortical thickness and > cortical surface

[Freesurfer] Cortical thickness values on a vertex base level

External Email - Use Caution Dear developers, For a case-control study we are comparing the cortical thickness and cortical surface area on a vertex-base level, for which we found significant differences throughout the brain. Is it possible that, in addition to the significance

Re: [Freesurfer] Cortical thickness (spc) extraction

You can run corrections for multiple comparisons (mri_glmfit-sim) to get clusters of significant effects, then compute the mean over those clusters. On 9/19/19 8:08 AM, AKUDJEDU, THEOPHILUS wrote: > > External Email - Use Caution > > > Dear FreeSurfer, > > I used QDEC for the longitudinal

[Freesurfer] Cortical thickness (spc) extraction

External Email - Use Caution Dear FreeSurfer, I used QDEC for the longitudinal two‐stage model analyses, where temporal data within each subject was reduced to a symmetrised percent rate of change (spc) maps using the long_mris_slopes function for data acquired at two time-point

Re: [Freesurfer] Cortical Thickness Extraction

Hi Emma in principle of volume is proportional to ICV you would need to scale the thickness by (ICV)^(1/3). In practice we find that scaling the thickness doesn't really change the variance and loses you a DOF so we don't usually do it. cheers Bruce On Sat, 11 May 2019, Bunting, Emma wrote

Re: [Freesurfer] Cortical Thickness Extraction

External Email - Use Caution Hi Doug, Why should we not scale the thickness by the ICV? This is what we had thought to be the norm based on the literature, How would you advise normalising these values instead? Best wishes, Emma Greve, Douglas N.,Ph.D.

Re: [Freesurfer] Cortical thickness values more than 5 mm

sure, you need to rerun mris_thickness with -max where N is the threshold you want to use (making it big enough and nothing will get thresholded) On Fri, 5 Apr 2019, Gonzalo Rojas Costa wrote: External Email - Use Caution Hi: How can I get cortical thickness surface image

[Freesurfer] Cortical thickness values more than 5 mm

External Email - Use Caution Hi: How can I get cortical thickness surface image with values more than 5 mm? Sincerely Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mail.nmr.mgh.harvard.edu/mail

Re: [Freesurfer] cortical thickness values in the insula...

probably easiest to use matlab. see FREESURFER_HOME/matlab/read_annotation.m, which has an example On 4/5/2019 11:29 AM, Gonzalo Rojas Costa wrote: > External Email - Use Caution > > Hi: > >How can I get the different values of cortical thickness in the > insula? Not the mean and SD.

[Freesurfer] cortical thickness values in the insula...

External Email - Use Caution Hi: How can I get the different values of cortical thickness in the insula? Not the mean and SD... Sincerely Gonzalo Rojas Costa ___ Freesurfer mailing list Freesurfer@nmr.mgh.harvard.edu https://mai

Re: [Freesurfer] Cortical thickness values extraction issue

External Email - Use Caution THank you so much for your help! Le lun. 18 mars 2019 à 16:32, Greve, Douglas N.,Ph.D. < dgr...@mgh.harvard.edu> a écrit : > The vertices chosen for the cluster depend only on the cluster forming > threshold (CFT). Once that is chosen, the vertices in

Re: [Freesurfer] Cortical thickness values extraction issue

The vertices chosen for the cluster depend only on the cluster forming threshold (CFT). Once that is chosen, the vertices in the cluster are fixed. The permutation judges how likely the cluster as a whole would be seen by chance. There are other ways to do permutation, but this is the way we do

Re: [Freesurfer] Cortical thickness values extraction issue

External Email - Use Caution Ok, well then I do not understand the purpose of the permutation testing if the number of permutation would not change the size of the clusters. What is it doing if not refining what vertices are significant? Perhaps I am just missing a key idea. Best,

Re: [Freesurfer] Cortical Thickness Extraction

They do not have any normalization applied. BTW, you should not scale the thickness by the ICV On 3/18/19 10:24 AM, Bunting, Emma wrote: External Email - Use Caution Hi Freesurfer experts, I used a script created by ENIGMA to extract the cortical thickness values for 129 subjects that

[Freesurfer] Cortical Thickness Extraction

External Email - Use Caution Hi Freesurfer experts, I used a script created by ENIGMA to extract the cortical thickness values for 129 subjects that had undergone reconall processing. We are using these values in VBM analysis. From reading other papers, we notice that all regi

Re: [Freesurfer] Cortical thickness values extraction issue

The size of the cluster is not going to be affected by the number of iterations (only by the threshold). Why would you think that the cluster size is affected by the number of iterations? On 3/14/19 5:45 AM, Giuliana Klencklen wrote: > > External Email - Use Caution > > Hi Douglas, > > A

Re: [Freesurfer] Cortical thickness values extraction issue

External Email - Use Caution Hi Douglas, According to your suggestion, I used the permutation simulation approach. I chose a cluster forming threshold set at 0.05 and explored how the number of iterations effects the data. For example, I used this command for 1,000 iterations: mr

Re: [Freesurfer] Cortical thickness values extraction issue

You can make the bonferroni correction from of mri_glmfit-sim the same as qdec by not including --2spaces (the bonferroni correction in qdec is actually 1, not 0). Also, if you want to use such a low cluster forming threshold (1.3=p<.05), then you should use permutation and not MC (MC is not val

Re: [Freesurfer] Cortical thickness values extraction issue

This can happen if the label is small and/or you've used a lot of smoothing. It is better to do this kind of thing in fsaverage space rather than moving the labels back to the individual space. If you've run mri_glmfit-sim, then it should have created a table file (something.y.ocn.dat). This fi

[Freesurfer] Cortical thickness values extraction issue

External Email - Use Caution Hi FS experts, I did group-level, surface-based, vertex-wise analysis for baseline and longitudinal data. I used Qdec and do the same work with the fsgd version (mri_glmfit-sim command) to double-check the data. I created label files with tksurfer for

Re: [Freesurfer] cortical thickness calculation based on hammersmith segmentation

External Email - Use Caution Hi Bruce, thank you for your quick answer. I managed it now to create cannot files based on the atlas volumetric segmentations. I first created: mri_vol2surf —src .../Hammers_mith_atlas_n30r83_SPM5.nii --out .../Hammers_AVG.nii --out_type mgh --he

Re: [Freesurfer] cortical thickness calculation based on hammersmith segmentation

Hi Boris vol2surf samples a scalar overlay in the volume to be a scalar overlay on the surface. This is NOT the same as a surface itself - it contains no geometry or topology information. Try giving freeview a surface (which I guess you have for subject 0021). Something like freeview -f \ 00

Re: [Freesurfer] cortical thickness calculation based on hammersmith segmentation

External Email - Use Caution Hi, I used the following commands: mri_vol2surf —src .../Hammers_mith_atlas_n30r83_SPM5.nii --out lhHammers_mith_atlas_n30r83_SPM5surf.mgh --out_type mgh --hemi lh --regheader 0021 srcvol = .../Hammers_mith_atlas_n30r83_SPM5.nii srcreg unspecifie

Re: [Freesurfer] cortical thickness calculation based on hammersmith segmentation

Those are the commands. Can you send the command lines you used and a fuller description of exactly how it is not working? On 1/25/19 10:56 AM, Boris Rauchmann wrote: External Email - Use Caution Dear FreeSurfer Developers, I´m trying to extract the cortical thickness of individuals fro

[Freesurfer] cortical thickness calculation based on hammersmith segmentation

External Email - Use Caution <>Dear FreeSurfer Developers, I´m trying to extract the cortical thickness of individuals from a study cohort based on an hammersmith n30r83 atlas segmentation. I have this atlas only in as a volumetric file. I already run recon-all on all subjec

Re: [Freesurfer] Cortical Thickness at Individual Vertices (fwd)

o: Bruce Fischl > Cc: freesurfer@nmr.mgh.harvard.edu > Subject: Re: [Freesurfer] Cortical Thickness at Individual Vertices > > > External Email - Use Caution > > Hi Bruce! > James: I don't have any particular deep thoughts except, all things equal, > i

Re: [Freesurfer] Cortical Thickness at Individual Vertices (fwd)

from Tom -- Forwarded message -- Date: Thu, 12 Jul 2018 16:51:31 +0100 From: Thomas Nichols To: Bruce Fischl Cc: freesurfer@nmr.mgh.harvard.edu Subject: Re: [Freesurfer] Cortical Thickness at Individual Vertices External Email - Use Caution Hi Bruce

Re: [Freesurfer] Cortical Thickness at Individual Vertices

Hi James you could use techniques that compare the whole distribution of thicknesses across subject populations. You could do a t-test or something non-parametric like a Kolmogorov-Smirnov or use permutation testing. I'll cc Tom Nichols so he can chime in with something more sophisticated or

[Freesurfer] Cortical Thickness at Individual Vertices

External Email - Use Caution All, I am comparing cortical thickness between subjects with and without mild traumatic brain injury (mTBI). So far the contrasts in QDEC have not been significant after correcting for multiple comparisons. I am not necessarily surprised at this due to

Re: [Freesurfer] Cortical Thickness Using N30R83 Atlas

There are files called lh.area and lh.volume that you can use instead of lh.thickness. Make sure to use the --jac flag when applying mri_surf2surf to area or volume (but not thickness). This applies jacobian correction to preserve the total area or volume. When you run mri_segstats, include the

Re: [Freesurfer] Cortical Thickness Using N30R83 Atlas

External Email - Use Caution Hi again Doug, Sorry for not realizing this earlier, but I actually found a workflow that you created, which outlines the steps really well. (https://surfer.nmr.mgh.harvard.edu/fswiki/VolumeRoiCorticalThickness) However, instead of 'fsaverage' I us

Re: [Freesurfer] Cortical Thickness Using N30R83 Atlas

You can create an annotation with mris_seg2annot and then view it in freeview. Run it with --help to get docs On 06/14/2018 02:18 PM, Ryan Flores wrote: > External Email - Use Caution > > Great. That seemed to have worked. Is there a way to inspect that the ROIs > have been correctly p

Re: [Freesurfer] Cortical Thickness Using N30R83 Atlas

External Email - Use Caution Great. That seemed to have worked. Is there a way to inspect that the ROIs have been correctly placed? Perhaps by using freeview? Best, Ryan -- Ryan Flores Clinical Research Coordinator On 6/14/18, 11:02 AM, "freesurfer-boun...@nmr.mgh.harvard.edu

Re: [Freesurfer] Cortical Thickness Using N30R83 Atlas

The --trgsurfval is just the output (ie, lh.atlas.nii.gz sampled onto the surface of the subject). Use nii.gz or mgz for the output (not img). On 06/14/2018 01:46 PM, Ryan Flores wrote: > External Email - Use Caution > > Thank you for your response. Just to clarify, the first command sh

Re: [Freesurfer] Cortical Thickness Using N30R83 Atlas

External Email - Use Caution Thank you for your response. Just to clarify, the first command should be mri_vol2surf, correct? It appears to have worked; however, I'm not sure what my --trgsurfval should be? I'm trying the following commands, where mni is the subject directory fo

Re: [Freesurfer] Cortical Thickness Using N30R83 Atlas

You can always get info by running the command with --help. mri_vol2vol --mov atlas.nii.gz --regheader subject --hemi lh --projfrac-max 0 1 .1 --o lh.atlas.nii.gz This assumes that the atlas is in registration with the mni152 (you can test with tkregister --mov atlas.nii.gz --s subject --reghea

[Freesurfer] Cortical Thickness Using N30R83 Atlas

External Email - Use Caution Hello all, I am hoping to obtain structural information (e.g., cortical thickness, surface area, and volume) based on the n30r83 (aka Hammersmith) atlas, which is in MNI space. The atlas differentiates between the hemispheres by using odd/even numbe

Re: [Freesurfer] Cortical thickness and cortical stroke

on behalf of Bruce Fischl Sent: Thursday, May 31, 2018 1:09 PM To: Freesurfer support list Subject: Re: [Freesurfer] Cortical thickness and cortical stroke   Hi Guillaume I certainly wouldn't trust the thickness values anywhere near the lesion. What exactly are you trying to compute? c

Re: [Freesurfer] Cortical thickness and cortical stroke

-lesional hemisphere ? Regards Guillaume From: freesurfer-boun...@nmr.mgh.harvard.edu on behalf of Bruce Fischl Sent: Thursday, May 31, 2018 1:09 PM To: Freesurfer support list Subject: Re: [Freesurfer] Cortical thickness and cortical stroke Hi Guillaume I

Re: [Freesurfer] Cortical thickness and cortical stroke

Hi Guillaume I certainly wouldn't trust the thickness values anywhere near the lesion. What exactly are you trying to compute? cheers Bruce On Thu, 31 May 2018, Guillaume Bellanger wrote: External Email - Use Caution Hi Freesurfers users, I am looking on cortical thickne

Re: [Freesurfer] cortical thickness smoothing

fwhm) as well as measure the smoothness. The --smooth-only says to not do the FWHM estimate (just smooth it). > > Thanks in advance! > J > > > > > > >> Original Message >> Subject: Re: [Freesurfer] cortical thickness smoothing

Re: [Freesurfer] cortical thickness smoothing

moothness. The --smooth-only says to not do the FWHM estimate (just smooth it). > > Thanks in advance! > J > > > > > > >> Original Message >> Subject: Re: [Freesurfer] cortical thickness smoothing >> Local Time: December

Re: [Freesurfer] Cortical thickness clarification

Hi Eli, because the "closest" metric isn't symmetric. White-->Pial != pial-->white cheers Bruce On Tue, 12 Dec 2017, Rockers, Elijah D. wrote: > Hello, > > I was hoping to get some clarification on how exactly the cortical thickness > number is calculated. > In the videos, Doug says it's "th

[Freesurfer] Cortical thickness clarification

Hello, I was hoping to get some clarification on how exactly the cortical thickness number is calculated. In the videos, Doug says it's "the distance between the vertex on the white to the vertex on the pial, and you go backwards and forwards to compute the average thickness", and the 2000 pape

Re: [Freesurfer] cortical thickness smoothing

developed to measure the FWHM but I extended it to be able to apply smoothing (--fwhm) as well as measure the smoothness. The --smooth-only says to not do the FWHM estimate (just smooth it). > > Thanks in advance! > J > > > > > > >> Original Message ---

Re: [Freesurfer] cortical thickness smoothing

To reinforce what bruce is saying, mri_surf2surf does surface-based smoothing (ie, along the cortical surface), whereas fslmaths does volume-based smoothing which does not take into account the anatomy On 12/12/2017 10:38 AM, Bruce Fischl wrote: > Hi John > > I don't think fslmaths takes a surf

Re: [Freesurfer] cortical thickness smoothing

Thanks in advance! J > Original Message ---- > Subject: Re: [Freesurfer] cortical thickness smoothing > Local Time: December 12, 2017 10:38 AM > UTC Time: December 12, 2017 3:38 PM > From: fis...@nmr.mgh.harvard.edu > To: John Anderson , Freesurfer support list > >

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